Starting phenix.real_space_refine on Tue Dec 31 09:10:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xtg_33448/12_2024/7xtg_33448_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xtg_33448/12_2024/7xtg_33448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xtg_33448/12_2024/7xtg_33448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xtg_33448/12_2024/7xtg_33448.map" model { file = "/net/cci-nas-00/data/ceres_data/7xtg_33448/12_2024/7xtg_33448_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xtg_33448/12_2024/7xtg_33448_neut.cif" } resolution = 2.2 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= 0.002 sd= 0.089 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10110 2.51 5 N 2544 2.21 5 O 2697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15435 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 307 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "B" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "C" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 307 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "D" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1784 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 239} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2322 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 287} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "G" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 307 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "H" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1784 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 239} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2322 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 287} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "Y" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1784 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 239} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2322 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 287} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.57, per 1000 atoms: 0.62 Number of scatterers: 15435 At special positions: 0 Unit cell: (129.868, 127.338, 101.196, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2697 8.00 N 2544 7.00 C 10110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 15 " distance=2.04 Simple disulfide: pdb=" SG CYS C 10 " - pdb=" SG CYS C 15 " distance=2.04 Simple disulfide: pdb=" SG CYS G 10 " - pdb=" SG CYS G 15 " distance=2.04 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: 3.75 Conformation dependent library (CDL) restraints added in 2.1 seconds 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 3 sheets defined 75.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 18 through 41 removed outlier: 3.822A pdb=" N MET A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 19 Processing helix chain 'B' and resid 21 through 27 removed outlier: 3.774A pdb=" N ASP B 27 " --> pdb=" O LYS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.628A pdb=" N LEU B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.742A pdb=" N VAL B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 40 removed outlier: 3.846A pdb=" N MET C 30 " --> pdb=" O ILE C 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 25 removed outlier: 3.550A pdb=" N ILE D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 44 removed outlier: 3.856A pdb=" N THR D 37 " --> pdb=" O VAL D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 60 removed outlier: 3.747A pdb=" N CYS D 49 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET D 58 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 removed outlier: 3.660A pdb=" N SER D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 101 removed outlier: 3.845A pdb=" N ILE D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 134 removed outlier: 3.561A pdb=" N ILE D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D 129 " --> pdb=" O HIS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 164 removed outlier: 3.737A pdb=" N ILE D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY D 151 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) Proline residue: D 157 - end of helix Processing helix chain 'D' and resid 165 through 175 removed outlier: 3.692A pdb=" N GLU D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 189 removed outlier: 3.580A pdb=" N LEU D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 202 removed outlier: 3.856A pdb=" N GLY D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 219 Processing helix chain 'D' and resid 225 through 249 removed outlier: 3.582A pdb=" N GLN D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 19 Processing helix chain 'E' and resid 20 through 22 No H-bonds generated for 'chain 'E' and resid 20 through 22' Processing helix chain 'E' and resid 32 through 40 Processing helix chain 'E' and resid 40 through 48 removed outlier: 4.311A pdb=" N LYS E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 61 Processing helix chain 'E' and resid 72 through 88 Processing helix chain 'E' and resid 95 through 117 removed outlier: 3.588A pdb=" N LYS E 101 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY E 106 " --> pdb=" O VAL E 102 " (cutoff:3.500A) Proline residue: E 107 - end of helix Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 119 through 134 removed outlier: 3.610A pdb=" N LEU E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 166 removed outlier: 3.798A pdb=" N ILE E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN E 159 " --> pdb=" O THR E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 201 removed outlier: 4.000A pdb=" N LYS E 183 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL E 201 " --> pdb=" O VAL E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 Processing helix chain 'E' and resid 253 through 261 removed outlier: 3.934A pdb=" N LEU E 260 " --> pdb=" O ASN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 279 Processing helix chain 'E' and resid 282 through 300 removed outlier: 3.653A pdb=" N GLY E 294 " --> pdb=" O LEU E 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 19 removed outlier: 3.507A pdb=" N ASN F 9 " --> pdb=" O TYR F 5 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER F 10 " --> pdb=" O LYS F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 27 removed outlier: 3.677A pdb=" N ILE F 25 " --> pdb=" O ASN F 21 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS F 26 " --> pdb=" O PRO F 22 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP F 27 " --> pdb=" O LYS F 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 21 through 27' Processing helix chain 'F' and resid 27 through 42 removed outlier: 3.627A pdb=" N LEU F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 65 Processing helix chain 'F' and resid 70 through 76 removed outlier: 3.766A pdb=" N VAL F 74 " --> pdb=" O PRO F 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 41 Processing helix chain 'H' and resid 4 through 25 removed outlier: 3.569A pdb=" N ILE H 9 " --> pdb=" O PHE H 5 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU H 24 " --> pdb=" O VAL H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 44 removed outlier: 3.681A pdb=" N THR H 37 " --> pdb=" O VAL H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 60 removed outlier: 3.832A pdb=" N CYS H 49 " --> pdb=" O ASN H 45 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET H 58 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 88 removed outlier: 3.529A pdb=" N ALA H 77 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 134 removed outlier: 3.581A pdb=" N ILE H 101 " --> pdb=" O SER H 97 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL H 103 " --> pdb=" O ILE H 99 " (cutoff:3.500A) Proline residue: H 104 - end of helix removed outlier: 4.250A pdb=" N THR H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE H 123 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL H 124 " --> pdb=" O ALA H 120 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA H 129 " --> pdb=" O HIS H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 164 removed outlier: 3.829A pdb=" N TRP H 142 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET H 149 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN H 150 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY H 151 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE H 154 " --> pdb=" O GLN H 150 " (cutoff:3.500A) Proline residue: H 157 - end of helix Processing helix chain 'H' and resid 165 through 175 removed outlier: 3.579A pdb=" N VAL H 169 " --> pdb=" O GLY H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 189 removed outlier: 3.740A pdb=" N LEU H 184 " --> pdb=" O LEU H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 204 removed outlier: 3.805A pdb=" N GLY H 195 " --> pdb=" O VAL H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 219 Processing helix chain 'H' and resid 225 through 249 Processing helix chain 'I' and resid 8 through 19 Processing helix chain 'I' and resid 20 through 22 No H-bonds generated for 'chain 'I' and resid 20 through 22' Processing helix chain 'I' and resid 32 through 40 Processing helix chain 'I' and resid 40 through 48 removed outlier: 3.660A pdb=" N LYS I 46 " --> pdb=" O PRO I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 62 Processing helix chain 'I' and resid 72 through 88 Processing helix chain 'I' and resid 95 through 117 removed outlier: 3.754A pdb=" N LYS I 101 " --> pdb=" O ILE I 97 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY I 106 " --> pdb=" O VAL I 102 " (cutoff:3.500A) Proline residue: I 107 - end of helix Proline residue: I 114 - end of helix Processing helix chain 'I' and resid 119 through 134 removed outlier: 3.549A pdb=" N LEU I 131 " --> pdb=" O LEU I 127 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER I 134 " --> pdb=" O SER I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 166 removed outlier: 3.860A pdb=" N ILE I 141 " --> pdb=" O ILE I 137 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA I 153 " --> pdb=" O ALA I 149 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN I 159 " --> pdb=" O THR I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 173 removed outlier: 4.374A pdb=" N THR I 170 " --> pdb=" O SER I 167 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU I 171 " --> pdb=" O LYS I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 201 removed outlier: 4.128A pdb=" N LEU I 178 " --> pdb=" O SER I 174 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP I 180 " --> pdb=" O GLY I 176 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR I 182 " --> pdb=" O LEU I 178 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL I 201 " --> pdb=" O VAL I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 241 removed outlier: 3.541A pdb=" N SER I 234 " --> pdb=" O LYS I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 261 removed outlier: 3.556A pdb=" N LEU I 260 " --> pdb=" O ASN I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 263 through 279 removed outlier: 3.508A pdb=" N LEU I 269 " --> pdb=" O ALA I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 300 Processing helix chain 'J' and resid 4 through 19 Processing helix chain 'J' and resid 21 through 27 removed outlier: 3.508A pdb=" N LYS J 26 " --> pdb=" O PRO J 22 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP J 27 " --> pdb=" O LYS J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 43 Processing helix chain 'J' and resid 53 through 65 Processing helix chain 'J' and resid 70 through 76 removed outlier: 3.768A pdb=" N VAL J 74 " --> pdb=" O PRO J 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 25 removed outlier: 4.185A pdb=" N ILE Y 23 " --> pdb=" O GLY Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 44 Processing helix chain 'Y' and resid 45 through 60 removed outlier: 3.911A pdb=" N CYS Y 49 " --> pdb=" O ASN Y 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 73 through 88 Processing helix chain 'Y' and resid 94 through 134 removed outlier: 4.100A pdb=" N VAL Y 103 " --> pdb=" O ILE Y 99 " (cutoff:3.500A) Proline residue: Y 104 - end of helix removed outlier: 4.225A pdb=" N THR Y 121 " --> pdb=" O ARG Y 117 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY Y 122 " --> pdb=" O THR Y 118 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE Y 123 " --> pdb=" O LEU Y 119 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 164 removed outlier: 3.791A pdb=" N ILE Y 139 " --> pdb=" O ASN Y 135 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE Y 154 " --> pdb=" O GLN Y 150 " (cutoff:3.500A) Proline residue: Y 157 - end of helix Processing helix chain 'Y' and resid 165 through 175 Processing helix chain 'Y' and resid 177 through 189 removed outlier: 3.589A pdb=" N THR Y 181 " --> pdb=" O PRO Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 204 removed outlier: 3.951A pdb=" N GLY Y 195 " --> pdb=" O VAL Y 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 208 through 219 Processing helix chain 'Y' and resid 225 through 249 Processing helix chain 'Z' and resid 8 through 19 Processing helix chain 'Z' and resid 20 through 22 No H-bonds generated for 'chain 'Z' and resid 20 through 22' Processing helix chain 'Z' and resid 32 through 40 Processing helix chain 'Z' and resid 40 through 48 Processing helix chain 'Z' and resid 50 through 62 Processing helix chain 'Z' and resid 72 through 89 Processing helix chain 'Z' and resid 95 through 117 removed outlier: 4.009A pdb=" N GLY Z 106 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) Proline residue: Z 107 - end of helix Proline residue: Z 114 - end of helix Processing helix chain 'Z' and resid 119 through 134 removed outlier: 3.920A pdb=" N ILE Z 123 " --> pdb=" O THR Z 119 " (cutoff:3.500A) Processing helix chain 'Z' and resid 137 through 166 removed outlier: 3.970A pdb=" N ILE Z 141 " --> pdb=" O ILE Z 137 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY Z 166 " --> pdb=" O GLY Z 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 177 through 201 removed outlier: 3.885A pdb=" N VAL Z 201 " --> pdb=" O VAL Z 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 230 through 241 Processing helix chain 'Z' and resid 253 through 261 removed outlier: 3.728A pdb=" N LEU Z 260 " --> pdb=" O ASN Z 256 " (cutoff:3.500A) Processing helix chain 'Z' and resid 263 through 279 Processing helix chain 'Z' and resid 282 through 300 Processing sheet with id=AA1, first strand: chain 'E' and resid 208 through 210 removed outlier: 7.177A pdb=" N THR E 251 " --> pdb=" O VAL E 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 208 through 210 removed outlier: 6.756A pdb=" N THR I 251 " --> pdb=" O VAL I 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Z' and resid 208 through 210 removed outlier: 6.661A pdb=" N THR Z 251 " --> pdb=" O VAL Z 209 " (cutoff:3.500A) 1030 hydrogen bonds defined for protein. 3084 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.74 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4779 1.35 - 1.47: 3660 1.47 - 1.59: 7157 1.59 - 1.71: 1 1.71 - 1.83: 150 Bond restraints: 15747 Sorted by residual: bond pdb=" CG PRO Z 122 " pdb=" CD PRO Z 122 " ideal model delta sigma weight residual 1.503 1.331 0.172 3.40e-02 8.65e+02 2.56e+01 bond pdb=" CB PRO Z 122 " pdb=" CG PRO Z 122 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.94e+00 bond pdb=" CG PRO E 122 " pdb=" CD PRO E 122 " ideal model delta sigma weight residual 1.503 1.430 0.073 3.40e-02 8.65e+02 4.56e+00 bond pdb=" N PRO E 122 " pdb=" CD PRO E 122 " ideal model delta sigma weight residual 1.473 1.497 -0.024 1.40e-02 5.10e+03 2.86e+00 bond pdb=" CB PRO I 107 " pdb=" CG PRO I 107 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.10e+00 ... (remaining 15742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 21073 2.56 - 5.11: 261 5.11 - 7.67: 33 7.67 - 10.22: 6 10.22 - 12.78: 5 Bond angle restraints: 21378 Sorted by residual: angle pdb=" CA PRO Z 122 " pdb=" N PRO Z 122 " pdb=" CD PRO Z 122 " ideal model delta sigma weight residual 112.00 101.26 10.74 1.40e+00 5.10e-01 5.88e+01 angle pdb=" N PRO Z 122 " pdb=" CD PRO Z 122 " pdb=" CG PRO Z 122 " ideal model delta sigma weight residual 103.20 92.04 11.16 1.50e+00 4.44e-01 5.54e+01 angle pdb=" N VAL E 95 " pdb=" CA VAL E 95 " pdb=" C VAL E 95 " ideal model delta sigma weight residual 111.90 107.77 4.13 8.10e-01 1.52e+00 2.60e+01 angle pdb=" N VAL I 95 " pdb=" CA VAL I 95 " pdb=" C VAL I 95 " ideal model delta sigma weight residual 111.90 107.80 4.10 8.10e-01 1.52e+00 2.56e+01 angle pdb=" N PRO E 122 " pdb=" CD PRO E 122 " pdb=" CG PRO E 122 " ideal model delta sigma weight residual 103.20 95.64 7.56 1.50e+00 4.44e-01 2.54e+01 ... (remaining 21373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7875 17.94 - 35.87: 1039 35.87 - 53.81: 302 53.81 - 71.74: 64 71.74 - 89.68: 20 Dihedral angle restraints: 9300 sinusoidal: 3564 harmonic: 5736 Sorted by residual: dihedral pdb=" CA ARG Z 30 " pdb=" C ARG Z 30 " pdb=" N MET Z 31 " pdb=" CA MET Z 31 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA CYS G 10 " pdb=" C CYS G 10 " pdb=" N ASN G 11 " pdb=" CA ASN G 11 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA CYS A 10 " pdb=" C CYS A 10 " pdb=" N ASN A 11 " pdb=" CA ASN A 11 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 9297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1505 0.034 - 0.068: 757 0.068 - 0.102: 233 0.102 - 0.136: 62 0.136 - 0.171: 8 Chirality restraints: 2565 Sorted by residual: chirality pdb=" CG LEU Z 22 " pdb=" CB LEU Z 22 " pdb=" CD1 LEU Z 22 " pdb=" CD2 LEU Z 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA MET Y 149 " pdb=" N MET Y 149 " pdb=" C MET Y 149 " pdb=" CB MET Y 149 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA ILE E 92 " pdb=" N ILE E 92 " pdb=" C ILE E 92 " pdb=" CB ILE E 92 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 2562 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 71 " -0.090 5.00e-02 4.00e+02 1.36e-01 2.97e+01 pdb=" N PRO D 72 " 0.236 5.00e-02 4.00e+02 pdb=" CA PRO D 72 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO D 72 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Z 121 " -0.068 5.00e-02 4.00e+02 9.66e-02 1.49e+01 pdb=" N PRO Z 122 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO Z 122 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO Z 122 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP Y 209 " 0.059 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO Y 210 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO Y 210 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO Y 210 " 0.048 5.00e-02 4.00e+02 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 185 2.65 - 3.22: 15110 3.22 - 3.78: 25234 3.78 - 4.34: 34216 4.34 - 4.90: 54928 Nonbonded interactions: 129673 Sorted by model distance: nonbonded pdb=" OG SER E 234 " pdb=" OE1 GLN E 238 " model vdw 2.094 3.040 nonbonded pdb=" O PHE Z 154 " pdb=" OG1 THR Z 158 " model vdw 2.145 3.040 nonbonded pdb=" ND2 ASN G 6 " pdb=" O MET H 58 " model vdw 2.208 3.120 nonbonded pdb=" OG1 THR Z 206 " pdb=" O LEU Z 302 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLU E 84 " pdb=" OH TYR E 163 " model vdw 2.222 3.040 ... (remaining 129668 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'Y' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'Z' } 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 individual isotropic 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 35.160 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.090 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:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 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 : 0.004 0.172 15747 Z= 0.270 Angle : 0.764 12.779 21378 Z= 0.413 Chirality : 0.044 0.171 2565 Planarity : 0.007 0.136 2610 Dihedral : 18.198 89.676 5625 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.43 % Favored : 95.42 % Rotamer: Outliers : 2.55 % Allowed : 30.66 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.18), residues: 2010 helix: 0.28 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : -1.64 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Z 16 HIS 0.006 0.002 HIS E 298 PHE 0.018 0.002 PHE Z 21 TYR 0.018 0.002 TYR F 48 ARG 0.007 0.001 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 570 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: B 11 ILE cc_start: 0.8038 (mt) cc_final: 0.7837 (mt) REVERT: E 10 LYS cc_start: 0.7110 (ttmt) cc_final: 0.6862 (tptt) REVERT: E 122 PRO cc_start: 0.7699 (OUTLIER) cc_final: 0.7450 (Cg_exo) REVERT: E 247 ASP cc_start: 0.7816 (p0) cc_final: 0.7495 (p0) REVERT: Y 124 VAL cc_start: 0.7892 (OUTLIER) cc_final: 0.7673 (p) REVERT: Z 10 LYS cc_start: 0.7322 (ttmt) cc_final: 0.7069 (tptt) outliers start: 41 outliers final: 8 residues processed: 597 average time/residue: 1.2089 time to fit residues: 799.2123 Evaluate side-chains 300 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 290 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain E residue 122 PRO Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Z residue 50 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN C 6 ASN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 ASN E 238 GLN E 248 HIS H 150 GLN H 223 GLN I 23 GLN ** I 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 ASN ** I 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN I 179 GLN I 198 ASN I 239 GLN I 241 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 150 GLN Z 23 GLN Z 66 ASN Z 68 HIS Z 179 GLN Z 198 ASN Z 239 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15747 Z= 0.283 Angle : 0.725 8.833 21378 Z= 0.379 Chirality : 0.048 0.208 2565 Planarity : 0.006 0.108 2610 Dihedral : 5.206 50.773 2204 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.43 % Favored : 95.42 % Rotamer: Outliers : 6.53 % Allowed : 23.01 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.19), residues: 2010 helix: 1.39 (0.13), residues: 1467 sheet: None (None), residues: 0 loop : -1.65 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Z 26 HIS 0.009 0.002 HIS Y 30 PHE 0.018 0.002 PHE B 47 TYR 0.022 0.002 TYR H 144 ARG 0.007 0.001 ARG Z 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 371 time to evaluate : 1.907 Fit side-chains REVERT: B 39 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7066 (mm-30) REVERT: B 44 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.7012 (m-40) REVERT: E 10 LYS cc_start: 0.7651 (ttmt) cc_final: 0.7340 (tptm) REVERT: E 159 GLN cc_start: 0.8521 (tt0) cc_final: 0.8276 (tt0) REVERT: E 302 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8199 (mp) REVERT: G 19 ARG cc_start: 0.7202 (mpt90) cc_final: 0.6901 (mmm160) REVERT: I 10 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6863 (tptp) REVERT: I 31 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7444 (mtt) REVERT: I 63 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: I 159 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: I 241 GLN cc_start: 0.7268 (mt0) cc_final: 0.7054 (mp10) REVERT: J 7 LYS cc_start: 0.8153 (tttt) cc_final: 0.7914 (tttm) REVERT: J 68 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7616 (tt0) REVERT: Y 17 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8354 (mp) REVERT: Y 97 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.8180 (p) REVERT: Z 6 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7303 (tmmt) REVERT: Z 10 LYS cc_start: 0.7689 (ttmt) cc_final: 0.7449 (mptt) REVERT: Z 173 LEU cc_start: 0.4169 (OUTLIER) cc_final: 0.3705 (tm) REVERT: Z 183 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8525 (tptm) REVERT: Z 230 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7712 (mppt) outliers start: 105 outliers final: 27 residues processed: 438 average time/residue: 1.2657 time to fit residues: 611.4962 Evaluate side-chains 336 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 31 MET Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 159 GLN Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 97 SER Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 183 LYS Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 210 SER Chi-restraints excluded: chain Z residue 230 LYS Chi-restraints excluded: chain Z residue 241 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 0.0020 chunk 55 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS E 32 GLN E 98 GLN E 179 GLN H 125 HIS I 179 GLN I 237 GLN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Z 238 GLN Z 248 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.6280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15747 Z= 0.176 Angle : 0.568 7.933 21378 Z= 0.299 Chirality : 0.041 0.201 2565 Planarity : 0.005 0.083 2610 Dihedral : 4.435 25.494 2192 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.83 % Favored : 96.02 % Rotamer: Outliers : 4.23 % Allowed : 23.38 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.65 (0.19), residues: 2010 helix: 2.00 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -1.58 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 26 HIS 0.004 0.001 HIS Z 298 PHE 0.010 0.001 PHE I 161 TYR 0.010 0.001 TYR C 9 ARG 0.009 0.001 ARG Z 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 315 time to evaluate : 1.806 Fit side-chains REVERT: B 39 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7062 (mm-30) REVERT: B 40 GLU cc_start: 0.7834 (tp30) cc_final: 0.7608 (mm-30) REVERT: B 42 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7894 (mttm) REVERT: B 65 ASN cc_start: 0.7451 (t0) cc_final: 0.7202 (t0) REVERT: E 9 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7551 (tptt) REVERT: E 10 LYS cc_start: 0.7681 (ttmt) cc_final: 0.7372 (tptt) REVERT: E 159 GLN cc_start: 0.8599 (tt0) cc_final: 0.8331 (tt0) REVERT: F 42 LYS cc_start: 0.8119 (mtmm) cc_final: 0.7851 (mtmm) REVERT: G 19 ARG cc_start: 0.7235 (mpt90) cc_final: 0.6911 (mmm160) REVERT: I 10 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6837 (tptp) REVERT: I 31 MET cc_start: 0.7845 (mtt) cc_final: 0.7513 (mtt) REVERT: I 159 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: I 234 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8442 (t) REVERT: J 65 ASN cc_start: 0.7342 (t0) cc_final: 0.7120 (t0) REVERT: J 68 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7782 (tt0) REVERT: Y 17 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8384 (mp) REVERT: Z 6 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7511 (tppt) REVERT: Z 10 LYS cc_start: 0.7705 (ttmt) cc_final: 0.7495 (mptt) REVERT: Z 173 LEU cc_start: 0.4098 (OUTLIER) cc_final: 0.3676 (tm) REVERT: Z 230 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7683 (mppt) outliers start: 68 outliers final: 19 residues processed: 358 average time/residue: 1.3924 time to fit residues: 545.5291 Evaluate side-chains 318 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 291 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 159 GLN Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 230 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN F 65 ASN I 179 GLN I 237 GLN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 23 GLN Z 98 GLN Z 159 GLN Z 179 GLN Z 239 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 15747 Z= 0.229 Angle : 0.622 9.332 21378 Z= 0.328 Chirality : 0.044 0.229 2565 Planarity : 0.005 0.069 2610 Dihedral : 4.671 34.396 2191 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.23 % Favored : 95.62 % Rotamer: Outliers : 4.48 % Allowed : 22.01 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.75 (0.19), residues: 2010 helix: 2.04 (0.13), residues: 1491 sheet: None (None), residues: 0 loop : -1.53 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 26 HIS 0.006 0.001 HIS Y 28 PHE 0.010 0.002 PHE D 211 TYR 0.011 0.002 TYR B 14 ARG 0.012 0.001 ARG I 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 302 time to evaluate : 1.978 Fit side-chains REVERT: A 41 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7573 (ptt) REVERT: B 40 GLU cc_start: 0.7886 (tp30) cc_final: 0.7570 (mm-30) REVERT: B 65 ASN cc_start: 0.7661 (t0) cc_final: 0.7370 (t0) REVERT: C 30 MET cc_start: 0.8242 (mtp) cc_final: 0.7905 (ttm) REVERT: C 41 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7686 (ptt) REVERT: E 11 ASP cc_start: 0.7447 (m-30) cc_final: 0.7074 (m-30) REVERT: G 19 ARG cc_start: 0.7210 (mpt90) cc_final: 0.6908 (mmm160) REVERT: H 17 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8417 (mp) REVERT: I 10 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.6710 (tptp) REVERT: I 31 MET cc_start: 0.8090 (mtt) cc_final: 0.7643 (mtt) REVERT: J 40 GLU cc_start: 0.7897 (tp30) cc_final: 0.7470 (mm-30) REVERT: J 65 ASN cc_start: 0.7616 (t0) cc_final: 0.7323 (t0) REVERT: Y 17 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8504 (mp) REVERT: Y 25 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8626 (t70) REVERT: Z 6 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7506 (tmmt) REVERT: Z 10 LYS cc_start: 0.7713 (ttmt) cc_final: 0.7502 (mptt) REVERT: Z 173 LEU cc_start: 0.4117 (OUTLIER) cc_final: 0.3682 (tm) REVERT: Z 230 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7781 (mppt) outliers start: 72 outliers final: 29 residues processed: 352 average time/residue: 1.4140 time to fit residues: 544.2736 Evaluate side-chains 324 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 286 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 230 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN F 65 ASN I 179 GLN I 237 GLN Y 28 HIS ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Z 238 GLN Z 239 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15747 Z= 0.178 Angle : 0.562 8.031 21378 Z= 0.296 Chirality : 0.041 0.231 2565 Planarity : 0.005 0.063 2610 Dihedral : 4.478 27.844 2191 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.73 % Favored : 96.12 % Rotamer: Outliers : 3.36 % Allowed : 22.33 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.94 (0.19), residues: 2010 helix: 2.25 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -1.61 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 86 HIS 0.003 0.001 HIS Y 28 PHE 0.011 0.001 PHE E 161 TYR 0.010 0.001 TYR J 14 ARG 0.014 0.001 ARG I 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 297 time to evaluate : 1.575 Fit side-chains REVERT: A 41 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7605 (ptt) REVERT: B 39 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7147 (mm-30) REVERT: B 40 GLU cc_start: 0.7870 (tp30) cc_final: 0.7562 (mm-30) REVERT: B 65 ASN cc_start: 0.7608 (t0) cc_final: 0.7286 (t0) REVERT: C 30 MET cc_start: 0.8219 (mtp) cc_final: 0.7907 (ttm) REVERT: E 11 ASP cc_start: 0.7488 (m-30) cc_final: 0.7147 (m-30) REVERT: E 54 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7506 (mtt-85) REVERT: G 19 ARG cc_start: 0.7219 (mpt90) cc_final: 0.6947 (mmm160) REVERT: I 31 MET cc_start: 0.8053 (mtt) cc_final: 0.7640 (mtt) REVERT: I 237 GLN cc_start: 0.8579 (mt0) cc_final: 0.8190 (mt0) REVERT: I 241 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6918 (mp10) REVERT: I 303 MET cc_start: 0.8322 (mtt) cc_final: 0.7837 (mtt) REVERT: J 38 GLN cc_start: 0.8382 (tt0) cc_final: 0.8059 (tt0) REVERT: J 40 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: J 68 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7908 (mt-10) REVERT: Y 17 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8543 (mp) REVERT: Y 25 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8557 (t0) REVERT: Z 6 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7635 (tptp) REVERT: Z 10 LYS cc_start: 0.7681 (ttmt) cc_final: 0.7473 (mptt) REVERT: Z 173 LEU cc_start: 0.4125 (OUTLIER) cc_final: 0.3715 (tm) REVERT: Z 230 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7750 (mppt) outliers start: 54 outliers final: 23 residues processed: 332 average time/residue: 1.4934 time to fit residues: 541.0059 Evaluate side-chains 318 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 287 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain J residue 40 GLU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 97 SER Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 230 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN E 238 GLN I 61 HIS I 179 GLN J 65 ASN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Z 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.7287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 15747 Z= 0.332 Angle : 0.701 11.180 21378 Z= 0.371 Chirality : 0.048 0.293 2565 Planarity : 0.005 0.065 2610 Dihedral : 4.969 47.082 2191 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.03 % Favored : 95.67 % Rotamer: Outliers : 4.73 % Allowed : 21.46 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.19), residues: 2010 helix: 1.94 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -1.62 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 26 HIS 0.007 0.002 HIS Y 28 PHE 0.014 0.002 PHE D 211 TYR 0.028 0.002 TYR C 9 ARG 0.018 0.001 ARG I 164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 295 time to evaluate : 1.586 Fit side-chains REVERT: A 41 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7698 (ptt) REVERT: B 39 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7141 (mm-30) REVERT: B 40 GLU cc_start: 0.7875 (tp30) cc_final: 0.7619 (mm-30) REVERT: C 30 MET cc_start: 0.8297 (mtp) cc_final: 0.7958 (ttm) REVERT: C 41 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7814 (ptt) REVERT: E 11 ASP cc_start: 0.7576 (m-30) cc_final: 0.7231 (m-30) REVERT: E 152 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8246 (mtt) REVERT: E 159 GLN cc_start: 0.8730 (tt0) cc_final: 0.8432 (tt0) REVERT: E 169 ILE cc_start: 0.7108 (OUTLIER) cc_final: 0.6722 (pp) REVERT: H 176 MET cc_start: 0.8558 (tpp) cc_final: 0.8309 (mmm) REVERT: I 31 MET cc_start: 0.8240 (mtt) cc_final: 0.7756 (mtt) REVERT: I 164 ARG cc_start: 0.7417 (mtm110) cc_final: 0.7161 (mtm110) REVERT: I 237 GLN cc_start: 0.8643 (mt0) cc_final: 0.8267 (mt0) REVERT: I 241 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.7027 (mp10) REVERT: I 303 MET cc_start: 0.8375 (mtt) cc_final: 0.7834 (mtt) REVERT: J 38 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: J 40 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7402 (mm-30) REVERT: Y 25 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8645 (t70) REVERT: Y 92 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7407 (mppt) REVERT: Z 10 LYS cc_start: 0.7657 (ttmt) cc_final: 0.7449 (tptt) REVERT: Z 173 LEU cc_start: 0.4312 (OUTLIER) cc_final: 0.3907 (tm) REVERT: Z 230 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7868 (mppt) outliers start: 76 outliers final: 41 residues processed: 341 average time/residue: 1.4682 time to fit residues: 546.2632 Evaluate side-chains 344 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 292 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 40 GLU Chi-restraints excluded: chain J residue 86 TRP Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 92 LYS Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 132 LYS Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 130 SER Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 230 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN I 179 GLN J 65 ASN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Z 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.7327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 15747 Z= 0.215 Angle : 0.606 9.883 21378 Z= 0.320 Chirality : 0.043 0.264 2565 Planarity : 0.005 0.058 2610 Dihedral : 4.751 38.630 2191 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.73 % Favored : 96.12 % Rotamer: Outliers : 3.42 % Allowed : 22.64 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.84 (0.19), residues: 2010 helix: 2.15 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.62 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 26 HIS 0.004 0.001 HIS Y 28 PHE 0.010 0.001 PHE E 161 TYR 0.011 0.001 TYR B 14 ARG 0.013 0.001 ARG I 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 293 time to evaluate : 1.780 Fit side-chains REVERT: A 41 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7754 (ptt) REVERT: B 39 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7127 (mm-30) REVERT: B 40 GLU cc_start: 0.7873 (tp30) cc_final: 0.7646 (mm-30) REVERT: C 30 MET cc_start: 0.8265 (mtp) cc_final: 0.7953 (ttm) REVERT: E 11 ASP cc_start: 0.7544 (m-30) cc_final: 0.7260 (m-30) REVERT: E 169 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6775 (pp) REVERT: I 31 MET cc_start: 0.8107 (mtt) cc_final: 0.7693 (mtt) REVERT: I 164 ARG cc_start: 0.7404 (mtm110) cc_final: 0.7093 (mpt-90) REVERT: I 178 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8273 (mp) REVERT: I 237 GLN cc_start: 0.8597 (mt0) cc_final: 0.8286 (mt0) REVERT: I 241 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6981 (mp10) REVERT: Y 25 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8574 (t70) REVERT: Z 10 LYS cc_start: 0.7659 (ttmt) cc_final: 0.7443 (mptt) REVERT: Z 173 LEU cc_start: 0.4285 (OUTLIER) cc_final: 0.3883 (tm) REVERT: Z 230 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7852 (mppt) REVERT: Z 250 ILE cc_start: 0.8832 (mm) cc_final: 0.8604 (mt) outliers start: 55 outliers final: 35 residues processed: 331 average time/residue: 1.4880 time to fit residues: 536.8857 Evaluate side-chains 325 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 283 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 230 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN I 179 GLN J 65 ASN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Z 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.7335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15747 Z= 0.182 Angle : 0.578 10.231 21378 Z= 0.303 Chirality : 0.042 0.256 2565 Planarity : 0.005 0.054 2610 Dihedral : 4.593 28.258 2191 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.83 % Favored : 96.02 % Rotamer: Outliers : 3.11 % Allowed : 22.64 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.00 (0.19), residues: 2010 helix: 2.27 (0.13), residues: 1482 sheet: None (None), residues: 0 loop : -1.55 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 26 HIS 0.003 0.001 HIS Y 28 PHE 0.011 0.001 PHE E 161 TYR 0.011 0.001 TYR J 14 ARG 0.013 0.001 ARG Z 164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 294 time to evaluate : 1.697 Fit side-chains REVERT: A 41 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7736 (ptt) REVERT: B 39 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7149 (mm-30) REVERT: B 40 GLU cc_start: 0.7840 (tp30) cc_final: 0.7624 (mm-30) REVERT: C 30 MET cc_start: 0.8197 (mtp) cc_final: 0.7917 (ttm) REVERT: E 11 ASP cc_start: 0.7530 (m-30) cc_final: 0.7292 (m-30) REVERT: E 52 GLU cc_start: 0.7187 (mp0) cc_final: 0.6978 (pm20) REVERT: E 169 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6750 (pp) REVERT: I 31 MET cc_start: 0.8112 (mtt) cc_final: 0.7716 (mtt) REVERT: I 164 ARG cc_start: 0.7342 (mtm110) cc_final: 0.7026 (mpt-90) REVERT: I 178 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8269 (mp) REVERT: J 40 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7653 (mm-30) REVERT: Y 25 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8596 (t0) REVERT: Z 10 LYS cc_start: 0.7726 (ttmt) cc_final: 0.7524 (tptt) REVERT: Z 173 LEU cc_start: 0.4231 (OUTLIER) cc_final: 0.3833 (tm) REVERT: Z 230 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7815 (mppt) REVERT: Z 250 ILE cc_start: 0.8786 (mm) cc_final: 0.8546 (mt) outliers start: 50 outliers final: 26 residues processed: 328 average time/residue: 1.4871 time to fit residues: 532.3144 Evaluate side-chains 317 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 285 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 44 ASN Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 230 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN I 179 GLN J 65 ASN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.7393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 15747 Z= 0.251 Angle : 0.644 11.435 21378 Z= 0.338 Chirality : 0.044 0.268 2565 Planarity : 0.005 0.060 2610 Dihedral : 4.806 35.227 2191 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.83 % Favored : 95.97 % Rotamer: Outliers : 3.11 % Allowed : 22.76 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.88 (0.19), residues: 2010 helix: 2.11 (0.13), residues: 1497 sheet: None (None), residues: 0 loop : -1.45 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 26 HIS 0.005 0.001 HIS Z 61 PHE 0.011 0.002 PHE E 161 TYR 0.017 0.002 TYR J 14 ARG 0.013 0.001 ARG Z 164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 288 time to evaluate : 1.871 Fit side-chains REVERT: A 41 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7735 (ptt) REVERT: B 40 GLU cc_start: 0.7880 (tp30) cc_final: 0.7654 (mm-30) REVERT: C 30 MET cc_start: 0.8263 (mtp) cc_final: 0.7930 (ttm) REVERT: E 11 ASP cc_start: 0.7542 (m-30) cc_final: 0.7298 (m-30) REVERT: E 52 GLU cc_start: 0.7268 (mp0) cc_final: 0.6952 (mp0) REVERT: E 169 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.6914 (pp) REVERT: H 176 MET cc_start: 0.8558 (tpp) cc_final: 0.8304 (mmm) REVERT: I 31 MET cc_start: 0.8186 (mtt) cc_final: 0.7746 (mtt) REVERT: I 164 ARG cc_start: 0.7368 (mtm110) cc_final: 0.7058 (mpt-90) REVERT: I 178 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8269 (mp) REVERT: Y 25 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8604 (t70) REVERT: Z 10 LYS cc_start: 0.7661 (ttmt) cc_final: 0.7446 (tptt) REVERT: Z 173 LEU cc_start: 0.4246 (OUTLIER) cc_final: 0.3795 (tm) REVERT: Z 230 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7822 (mppt) REVERT: Z 250 ILE cc_start: 0.8848 (mm) cc_final: 0.8641 (mt) outliers start: 50 outliers final: 37 residues processed: 325 average time/residue: 1.4701 time to fit residues: 522.0123 Evaluate side-chains 332 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 44 ASN Chi-restraints excluded: chain J residue 86 TRP Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 230 LYS Chi-restraints excluded: chain Z residue 241 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN ** I 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.7426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 15747 Z= 0.249 Angle : 0.647 11.297 21378 Z= 0.340 Chirality : 0.045 0.264 2565 Planarity : 0.005 0.058 2610 Dihedral : 4.824 36.954 2191 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.78 % Favored : 96.07 % Rotamer: Outliers : 2.80 % Allowed : 23.26 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.85 (0.19), residues: 2010 helix: 2.08 (0.13), residues: 1497 sheet: None (None), residues: 0 loop : -1.44 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 26 HIS 0.005 0.001 HIS Y 28 PHE 0.011 0.002 PHE E 161 TYR 0.018 0.002 TYR J 14 ARG 0.013 0.001 ARG Z 164 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 1.763 Fit side-chains REVERT: A 41 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7804 (ptt) REVERT: B 39 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7125 (mm-30) REVERT: B 40 GLU cc_start: 0.7879 (tp30) cc_final: 0.7658 (mm-30) REVERT: C 30 MET cc_start: 0.8273 (mtp) cc_final: 0.7958 (ttm) REVERT: E 11 ASP cc_start: 0.7526 (m-30) cc_final: 0.7298 (m-30) REVERT: E 52 GLU cc_start: 0.7269 (mp0) cc_final: 0.6961 (mp0) REVERT: E 169 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7057 (pp) REVERT: H 176 MET cc_start: 0.8562 (tpp) cc_final: 0.8302 (mmm) REVERT: I 31 MET cc_start: 0.8202 (mtt) cc_final: 0.7767 (mtt) REVERT: I 164 ARG cc_start: 0.7388 (mtm110) cc_final: 0.7063 (mpt-90) REVERT: I 178 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8208 (mp) REVERT: Y 25 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8607 (t70) REVERT: Z 10 LYS cc_start: 0.7658 (ttmt) cc_final: 0.7448 (tptt) REVERT: Z 173 LEU cc_start: 0.4210 (OUTLIER) cc_final: 0.3753 (tm) REVERT: Z 230 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7809 (mppt) REVERT: Z 250 ILE cc_start: 0.8848 (mm) cc_final: 0.8640 (mt) outliers start: 45 outliers final: 36 residues processed: 320 average time/residue: 1.5178 time to fit residues: 531.0963 Evaluate side-chains 329 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 287 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 44 ASN Chi-restraints excluded: chain J residue 86 TRP Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 202 SER Chi-restraints excluded: chain Z residue 230 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 157 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 138 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN F 65 ASN I 179 GLN J 65 ASN ** Y 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.130335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098474 restraints weight = 16733.602| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.36 r_work: 0.3075 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.7428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 15747 Z= 0.198 Angle : 0.600 10.563 21378 Z= 0.315 Chirality : 0.042 0.237 2565 Planarity : 0.005 0.055 2610 Dihedral : 4.661 29.570 2191 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.73 % Favored : 96.12 % Rotamer: Outliers : 2.80 % Allowed : 23.13 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.99 (0.19), residues: 2010 helix: 2.24 (0.13), residues: 1485 sheet: None (None), residues: 0 loop : -1.50 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 26 HIS 0.003 0.001 HIS Y 28 PHE 0.011 0.001 PHE E 161 TYR 0.016 0.001 TYR J 14 ARG 0.013 0.001 ARG Z 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8011.37 seconds wall clock time: 143 minutes 48.88 seconds (8628.88 seconds total)