Starting phenix.real_space_refine on Sun Sep 13 18:44:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6l4t_0834/09_2026/6l4t_0834.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l4t_0834/09_2026/6l4t_0834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6l4t_0834/09_2026/6l4t_0834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l4t_0834/09_2026/6l4t_0834.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6l4t_0834/09_2026/6l4t_0834.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6l4t_0834/09_2026/6l4t_0834.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6l4t_0834/09_2026/6l4t_0834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l4t_0834/09_2026/6l4t_0834.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 Mg 119 5.21 5 S 82 5.16 5 C 17161 2.51 5 N 2825 2.21 5 O 3675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23863 Number of models: 1 Model: "" Number of chains: 26 Chain: "6" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1354 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 162} Chain: "7" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1416 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain: "8" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1660 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 199} Chain: "10" Number of atoms: 1302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1302 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 151} Chain: "11" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1479 Classifications: {'peptide': 191} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 176} Chain: "12" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1274 Classifications: {'peptide': 173} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 158} Chain: "13" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1148 Classifications: {'peptide': 150} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 141} Chain breaks: 2 Chain: "14" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1609 Classifications: {'peptide': 208} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 187} Chain: "15" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1654 Classifications: {'peptide': 211} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 190} Chain: "16" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1313 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 158} Chain: "6" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 1004 Unusual residues: {'A86': 1, 'CLA': 10, 'DD6': 3, 'KC1': 4, 'LHG': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "7" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 1044 Unusual residues: {'A86': 3, 'CLA': 9, 'DD6': 4, 'KC1': 2, 'LMG': 1, 'LMT': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 4 Chain: "8" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 1130 Unusual residues: {'A86': 2, 'CLA': 7, 'DD6': 2, 'KC1': 7, 'LMG': 3, 'LMT': 3} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 3 Chain: "10" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 896 Unusual residues: {'A86': 5, 'CLA': 7, 'DD6': 2, 'KC1': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "11" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 800 Unusual residues: {'A86': 4, 'CLA': 5, 'DD6': 1, 'KC1': 4, 'LMT': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "12" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1103 Unusual residues: {'A86': 2, 'CLA': 9, 'DD6': 2, 'KC1': 4, 'LMT': 5} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 4 Chain: "13" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 756 Unusual residues: {'A86': 2, 'CLA': 6, 'DD6': 1, 'KC1': 6} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CLA:plan-5': 2, 'A86:plan-4': 1} Unresolved non-hydrogen planarities: 13 Chain: "14" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1073 Unusual residues: {'A86': 9, 'CLA': 9, 'KC1': 3, 'LMG': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'CLA:plan-5': 4} Unresolved non-hydrogen planarities: 19 Chain: "15" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1094 Unusual residues: {'A86': 6, 'CLA': 13, 'DD6': 2, 'LMT': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'CLA:plan-5': 7} Unresolved non-hydrogen planarities: 35 Chain: "16" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 742 Unusual residues: {'A86': 2, 'CLA': 9, 'DD6': 1, 'KC1': 2, 'LMT': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 4} Unresolved non-hydrogen planarities: 19 Chain: "6" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "8" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "10" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "11" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "12" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.62, per 1000 atoms: 0.19 Number of scatterers: 23863 At special positions: 0 Unit cell: (183.645, 129.108, 150.255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 82 16.00 P 1 15.00 Mg 119 11.99 O 3675 8.00 N 2825 7.00 C 17161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=138, symmetry=0 Number of additional bonds: simple=138, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 937.1 milliseconds 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 1 sheets defined 58.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain '6' and resid 46 through 50 removed outlier: 3.672A pdb=" N ALA 6 50 " --> pdb=" O GLU 6 47 " (cutoff:3.500A) Processing helix chain '6' and resid 62 through 66 Processing helix chain '6' and resid 68 through 94 removed outlier: 3.844A pdb=" N VAL 6 93 " --> pdb=" O GLY 6 89 " (cutoff:3.500A) Processing helix chain '6' and resid 113 through 121 removed outlier: 3.633A pdb=" N LEU 6 118 " --> pdb=" O ALA 6 114 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN 6 120 " --> pdb=" O ASP 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 148 removed outlier: 3.627A pdb=" N VAL 6 140 " --> pdb=" O ALA 6 136 " (cutoff:3.500A) Processing helix chain '6' and resid 169 through 202 removed outlier: 3.522A pdb=" N LYS 6 179 " --> pdb=" O GLU 6 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 6 189 " --> pdb=" O ARG 6 185 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA 6 198 " --> pdb=" O VAL 6 194 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL 6 199 " --> pdb=" O VAL 6 195 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 141 Processing helix chain '7' and resid 147 through 176 removed outlier: 3.565A pdb=" N VAL 7 167 " --> pdb=" O MET 7 163 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL 7 172 " --> pdb=" O GLY 7 168 " (cutoff:3.500A) Processing helix chain '7' and resid 188 through 200 removed outlier: 4.396A pdb=" N TRP 7 194 " --> pdb=" O MET 7 190 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN 7 195 " --> pdb=" O ASP 7 191 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE 7 196 " --> pdb=" O ALA 7 192 " (cutoff:3.500A) Processing helix chain '7' and resid 200 through 228 removed outlier: 4.313A pdb=" N ILE 7 204 " --> pdb=" O HIS 7 200 " (cutoff:3.500A) Processing helix chain '7' and resid 247 through 278 removed outlier: 3.971A pdb=" N PHE 7 267 " --> pdb=" O ARG 7 263 " (cutoff:3.500A) Processing helix chain '7' and resid 282 through 294 Processing helix chain '8' and resid 62 through 66 Processing helix chain '8' and resid 106 through 111 removed outlier: 3.586A pdb=" N PHE 8 110 " --> pdb=" O PHE 8 107 " (cutoff:3.500A) Processing helix chain '8' and resid 122 through 149 removed outlier: 3.552A pdb=" N LEU 8 140 " --> pdb=" O ARG 8 136 " (cutoff:3.500A) Processing helix chain '8' and resid 160 through 164 Processing helix chain '8' and resid 170 through 172 No H-bonds generated for 'chain '8' and resid 170 through 172' Processing helix chain '8' and resid 173 through 182 Processing helix chain '8' and resid 182 through 200 removed outlier: 3.855A pdb=" N ALA 8 200 " --> pdb=" O PHE 8 196 " (cutoff:3.500A) Processing helix chain '8' and resid 200 through 207 removed outlier: 3.596A pdb=" N GLU 8 204 " --> pdb=" O ALA 8 200 " (cutoff:3.500A) Processing helix chain '8' and resid 229 through 258 removed outlier: 3.516A pdb=" N THR 8 256 " --> pdb=" O GLY 8 252 " (cutoff:3.500A) Processing helix chain '10' and resid 62 through 67 Processing helix chain '10' and resid 70 through 91 Processing helix chain '10' and resid 93 through 97 Processing helix chain '10' and resid 112 through 114 No H-bonds generated for 'chain '10' and resid 112 through 114' Processing helix chain '10' and resid 115 through 120 removed outlier: 3.537A pdb=" N LEU10 120 " --> pdb=" O ALA10 116 " (cutoff:3.500A) Processing helix chain '10' and resid 120 through 137 removed outlier: 4.177A pdb=" N GLN10 126 " --> pdb=" O GLU10 122 " (cutoff:3.500A) Processing helix chain '10' and resid 138 through 143 Processing helix chain '10' and resid 167 through 199 removed outlier: 4.608A pdb=" N GLN10 173 " --> pdb=" O GLU10 169 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY10 190 " --> pdb=" O MET10 186 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR10 199 " --> pdb=" O GLY10 195 " (cutoff:3.500A) Processing helix chain '11' and resid 50 through 58 removed outlier: 4.250A pdb=" N ILE11 56 " --> pdb=" O LEU11 52 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU11 57 " --> pdb=" O GLY11 53 " (cutoff:3.500A) Processing helix chain '11' and resid 61 through 91 removed outlier: 3.599A pdb=" N ILE11 65 " --> pdb=" O GLN11 61 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE11 84 " --> pdb=" O MET11 80 " (cutoff:3.500A) Processing helix chain '11' and resid 124 through 129 removed outlier: 3.573A pdb=" N ILE11 128 " --> pdb=" O THR11 124 " (cutoff:3.500A) Processing helix chain '11' and resid 132 through 139 removed outlier: 4.241A pdb=" N ILE11 137 " --> pdb=" O PRO11 133 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN11 138 " --> pdb=" O LEU11 134 " (cutoff:3.500A) Processing helix chain '11' and resid 141 through 164 removed outlier: 3.582A pdb=" N GLN11 147 " --> pdb=" O ALA11 143 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER11 157 " --> pdb=" O GLY11 153 " (cutoff:3.500A) Processing helix chain '11' and resid 180 through 184 removed outlier: 3.763A pdb=" N LYS11 183 " --> pdb=" O GLY11 180 " (cutoff:3.500A) Processing helix chain '11' and resid 190 through 220 removed outlier: 3.557A pdb=" N MET11 209 " --> pdb=" O ARG11 205 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP11 217 " --> pdb=" O ALA11 213 " (cutoff:3.500A) Processing helix chain '12' and resid 55 through 86 removed outlier: 3.502A pdb=" N LEU12 75 " --> pdb=" O ARG12 71 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY12 86 " --> pdb=" O VAL12 82 " (cutoff:3.500A) Processing helix chain '12' and resid 98 through 104 removed outlier: 3.630A pdb=" N LEU12 102 " --> pdb=" O SER12 98 " (cutoff:3.500A) Processing helix chain '12' and resid 106 through 111 removed outlier: 3.607A pdb=" N TRP12 111 " --> pdb=" O PRO12 107 " (cutoff:3.500A) Processing helix chain '12' and resid 115 through 135 Processing helix chain '12' and resid 139 through 143 Processing helix chain '12' and resid 160 through 191 Processing helix chain '12' and resid 195 through 199 removed outlier: 4.052A pdb=" N THR12 199 " --> pdb=" O PRO12 196 " (cutoff:3.500A) Processing helix chain '13' and resid 61 through 66 Processing helix chain '13' and resid 88 through 117 removed outlier: 3.506A pdb=" N LEU13 92 " --> pdb=" O SER13 88 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA13 108 " --> pdb=" O ARG13 104 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL13 111 " --> pdb=" O MET13 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP13 114 " --> pdb=" O PHE13 110 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL13 116 " --> pdb=" O GLY13 112 " (cutoff:3.500A) Processing helix chain '13' and resid 140 through 145 Processing helix chain '13' and resid 147 through 172 removed outlier: 3.504A pdb=" N ALA13 152 " --> pdb=" O GLY13 148 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU13 156 " --> pdb=" O ALA13 152 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU13 166 " --> pdb=" O GLU13 162 " (cutoff:3.500A) Processing helix chain '13' and resid 207 through 231 removed outlier: 3.533A pdb=" N ASN13 217 " --> pdb=" O ARG13 213 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA13 221 " --> pdb=" O ASN13 217 " (cutoff:3.500A) Processing helix chain '14' and resid 42 through 52 removed outlier: 3.549A pdb=" N ALA14 46 " --> pdb=" O ASP14 42 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS14 50 " --> pdb=" O ALA14 46 " (cutoff:3.500A) Processing helix chain '14' and resid 62 through 66 Processing helix chain '14' and resid 72 through 103 removed outlier: 3.510A pdb=" N THR14 76 " --> pdb=" O THR14 72 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY14 78 " --> pdb=" O SER14 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN14 103 " --> pdb=" O ILE14 99 " (cutoff:3.500A) Processing helix chain '14' and resid 124 through 131 removed outlier: 3.849A pdb=" N ASP14 130 " --> pdb=" O PRO14 126 " (cutoff:3.500A) Processing helix chain '14' and resid 134 through 154 removed outlier: 4.148A pdb=" N TRP14 138 " --> pdb=" O ASP14 134 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN14 139 " --> pdb=" O ALA14 135 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU14 152 " --> pdb=" O GLU14 148 " (cutoff:3.500A) Processing helix chain '14' and resid 195 through 224 removed outlier: 3.727A pdb=" N ASP14 201 " --> pdb=" O ALA14 197 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY14 202 " --> pdb=" O GLN14 198 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU14 203 " --> pdb=" O LYS14 199 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE14 204 " --> pdb=" O ALA14 200 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU14 223 " --> pdb=" O GLY14 219 " (cutoff:3.500A) Processing helix chain '15' and resid 63 through 73 removed outlier: 3.607A pdb=" N LYS15 71 " --> pdb=" O ALA15 67 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN15 73 " --> pdb=" O ALA15 69 " (cutoff:3.500A) Processing helix chain '15' and resid 83 through 87 removed outlier: 3.674A pdb=" N ASP15 86 " --> pdb=" O SER15 83 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS15 87 " --> pdb=" O LEU15 84 " (cutoff:3.500A) No H-bonds generated for 'chain '15' and resid 83 through 87' Processing helix chain '15' and resid 93 through 117 removed outlier: 3.647A pdb=" N ALA15 99 " --> pdb=" O ASP15 95 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG15 102 " --> pdb=" O ILE15 98 " (cutoff:3.500A) Processing helix chain '15' and resid 144 through 148 removed outlier: 3.535A pdb=" N ALA15 147 " --> pdb=" O SER15 144 " (cutoff:3.500A) Processing helix chain '15' and resid 153 through 174 removed outlier: 3.765A pdb=" N GLN15 159 " --> pdb=" O GLY15 155 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER15 165 " --> pdb=" O PHE15 161 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU15 172 " --> pdb=" O GLU15 168 " (cutoff:3.500A) Processing helix chain '15' and resid 181 through 185 removed outlier: 3.698A pdb=" N GLY15 185 " --> pdb=" O TYR15 182 " (cutoff:3.500A) Processing helix chain '15' and resid 194 through 199 Processing helix chain '15' and resid 218 through 241 removed outlier: 4.139A pdb=" N LYS15 222 " --> pdb=" O SER15 218 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU15 223 " --> pdb=" O GLU15 219 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG15 224 " --> pdb=" O GLU15 220 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER15 228 " --> pdb=" O ARG15 224 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN15 231 " --> pdb=" O VAL15 227 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU15 235 " --> pdb=" O ASN15 231 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU15 238 " --> pdb=" O ARG15 234 " (cutoff:3.500A) Processing helix chain '15' and resid 242 through 243 No H-bonds generated for 'chain '15' and resid 242 through 243' Processing helix chain '15' and resid 244 through 248 removed outlier: 3.586A pdb=" N ASP15 247 " --> pdb=" O LEU15 244 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR15 248 " --> pdb=" O CYS15 245 " (cutoff:3.500A) No H-bonds generated for 'chain '15' and resid 244 through 248' Processing helix chain '16' and resid 69 through 99 removed outlier: 3.693A pdb=" N GLN16 97 " --> pdb=" O GLY16 93 " (cutoff:3.500A) Processing helix chain '16' and resid 112 through 119 removed outlier: 3.971A pdb=" N LEU16 116 " --> pdb=" O SER16 112 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA16 118 " --> pdb=" O GLU16 114 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N MET16 119 " --> pdb=" O SER16 115 " (cutoff:3.500A) Processing helix chain '16' and resid 120 through 125 removed outlier: 3.718A pdb=" N TRP16 125 " --> pdb=" O PRO16 121 " (cutoff:3.500A) Processing helix chain '16' and resid 126 through 128 No H-bonds generated for 'chain '16' and resid 126 through 128' Processing helix chain '16' and resid 129 through 148 Processing helix chain '16' and resid 174 through 204 removed outlier: 3.516A pdb=" N LYS16 179 " --> pdb=" O PRO16 175 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR16 180 " --> pdb=" O GLU16 176 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN16 187 " --> pdb=" O ASN16 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '8' and resid 67 through 72 removed outlier: 6.425A pdb=" N GLU 8 71 " --> pdb=" O ARG 8 81 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.35: 5960 1.35 - 1.53: 16988 1.53 - 1.72: 1743 1.72 - 1.90: 149 1.90 - 2.08: 476 Bond restraints: 25316 Sorted by residual: bond pdb=" C10 DD611 312 " pdb=" C11 DD611 312 " ideal model delta sigma weight residual 1.350 1.698 -0.348 2.00e-02 2.50e+03 3.04e+02 bond pdb=" C10 DD610 313 " pdb=" C11 DD610 313 " ideal model delta sigma weight residual 1.350 1.697 -0.347 2.00e-02 2.50e+03 3.02e+02 bond pdb=" C10 DD6 7 317 " pdb=" C11 DD6 7 317 " ideal model delta sigma weight residual 1.350 1.696 -0.346 2.00e-02 2.50e+03 2.99e+02 bond pdb=" C10 DD615 318 " pdb=" C11 DD615 318 " ideal model delta sigma weight residual 1.350 1.695 -0.345 2.00e-02 2.50e+03 2.97e+02 bond pdb=" C10 DD610 314 " pdb=" C11 DD610 314 " ideal model delta sigma weight residual 1.350 1.694 -0.344 2.00e-02 2.50e+03 2.95e+02 ... (remaining 25311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.50: 35486 9.50 - 19.00: 897 19.00 - 28.49: 84 28.49 - 37.99: 46 37.99 - 47.49: 44 Bond angle restraints: 36557 Sorted by residual: angle pdb=" C A86 8 318 " pdb=" C1 A86 8 318 " pdb=" C2 A86 8 318 " ideal model delta sigma weight residual 123.61 76.12 47.49 3.00e+00 1.11e-01 2.51e+02 angle pdb=" C29 DD615 319 " pdb=" C30 DD615 319 " pdb=" C31 DD615 319 " ideal model delta sigma weight residual 180.00 135.37 44.63 3.00e+00 1.11e-01 2.21e+02 angle pdb=" C29 DD611 312 " pdb=" C30 DD611 312 " pdb=" C31 DD611 312 " ideal model delta sigma weight residual 180.00 136.41 43.59 3.00e+00 1.11e-01 2.11e+02 angle pdb=" C29 DD612 317 " pdb=" C30 DD612 317 " pdb=" C31 DD612 317 " ideal model delta sigma weight residual 180.00 136.55 43.45 3.00e+00 1.11e-01 2.10e+02 angle pdb=" C29 DD612 315 " pdb=" C30 DD612 315 " pdb=" C31 DD612 315 " ideal model delta sigma weight residual 180.00 137.41 42.59 3.00e+00 1.11e-01 2.02e+02 ... (remaining 36552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 12095 35.91 - 71.81: 1287 71.81 - 107.71: 432 107.71 - 143.62: 54 143.62 - 179.52: 59 Dihedral angle restraints: 13927 sinusoidal: 8713 harmonic: 5214 Sorted by residual: dihedral pdb=" CA PRO10 204 " pdb=" C PRO10 204 " pdb=" N TYR10 205 " pdb=" CA TYR10 205 " ideal model delta harmonic sigma weight residual 180.00 130.44 49.56 0 5.00e+00 4.00e-02 9.82e+01 dihedral pdb=" CA SER15 264 " pdb=" C SER15 264 " pdb=" N GLY15 265 " pdb=" CA GLY15 265 " ideal model delta harmonic sigma weight residual 180.00 133.88 46.12 0 5.00e+00 4.00e-02 8.51e+01 dihedral pdb=" CA MET15 268 " pdb=" C MET15 268 " pdb=" N GLN15 269 " pdb=" CA GLN15 269 " ideal model delta harmonic sigma weight residual -180.00 -141.27 -38.73 0 5.00e+00 4.00e-02 6.00e+01 ... (remaining 13924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.359: 2803 0.359 - 0.719: 45 0.719 - 1.078: 21 1.078 - 1.437: 18 1.437 - 1.797: 36 Chirality restraints: 2923 Sorted by residual: chirality pdb=" C20 A86 6 317 " pdb=" C15 A86 6 317 " pdb=" C19 A86 6 317 " pdb=" C21 A86 6 317 " both_signs ideal model delta sigma weight residual True 1.08 2.87 -1.80 2.00e-01 2.50e+01 8.07e+01 chirality pdb=" C20 A8610 302 " pdb=" C15 A8610 302 " pdb=" C19 A8610 302 " pdb=" C21 A8610 302 " both_signs ideal model delta sigma weight residual True 1.08 2.83 -1.75 2.00e-01 2.50e+01 7.64e+01 chirality pdb=" C20 A8614 315 " pdb=" C15 A8614 315 " pdb=" C19 A8614 315 " pdb=" C21 A8614 315 " both_signs ideal model delta sigma weight residual True 1.08 2.82 -1.74 2.00e-01 2.50e+01 7.57e+01 ... (remaining 2920 not shown) Planarity restraints: 4475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A KC1 7 312 " 0.214 2.00e-02 2.50e+03 5.71e-01 8.14e+03 pdb=" C2A KC1 7 312 " 0.188 2.00e-02 2.50e+03 pdb=" C3A KC1 7 312 " -0.094 2.00e-02 2.50e+03 pdb=" C4A KC1 7 312 " -0.253 2.00e-02 2.50e+03 pdb=" CAA KC1 7 312 " -1.096 2.00e-02 2.50e+03 pdb=" CHA KC1 7 312 " 0.508 2.00e-02 2.50e+03 pdb=" CHB KC1 7 312 " -0.571 2.00e-02 2.50e+03 pdb=" CMA KC1 7 312 " 1.144 2.00e-02 2.50e+03 pdb=" NA KC1 7 312 " -0.072 2.00e-02 2.50e+03 pdb="MG KC1 7 312 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A KC1 8 313 " -0.198 2.00e-02 2.50e+03 5.60e-01 7.84e+03 pdb=" C2A KC1 8 313 " -0.192 2.00e-02 2.50e+03 pdb=" C3A KC1 8 313 " 0.098 2.00e-02 2.50e+03 pdb=" C4A KC1 8 313 " 0.258 2.00e-02 2.50e+03 pdb=" CAA KC1 8 313 " 1.051 2.00e-02 2.50e+03 pdb=" CHA KC1 8 313 " -0.488 2.00e-02 2.50e+03 pdb=" CHB KC1 8 313 " 0.571 2.00e-02 2.50e+03 pdb=" CMA KC1 8 313 " -1.143 2.00e-02 2.50e+03 pdb=" NA KC1 8 313 " 0.081 2.00e-02 2.50e+03 pdb="MG KC1 8 313 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A KC1 8 307 " -0.225 2.00e-02 2.50e+03 5.58e-01 7.79e+03 pdb=" C2A KC1 8 307 " -0.119 2.00e-02 2.50e+03 pdb=" C3A KC1 8 307 " 0.158 2.00e-02 2.50e+03 pdb=" C4A KC1 8 307 " 0.192 2.00e-02 2.50e+03 pdb=" CAA KC1 8 307 " 1.115 2.00e-02 2.50e+03 pdb=" CHA KC1 8 307 " -0.571 2.00e-02 2.50e+03 pdb=" CHB KC1 8 307 " 0.455 2.00e-02 2.50e+03 pdb=" CMA KC1 8 307 " -1.089 2.00e-02 2.50e+03 pdb=" NA KC1 8 307 " -0.065 2.00e-02 2.50e+03 pdb="MG KC1 8 307 " 0.150 2.00e-02 2.50e+03 ... (remaining 4472 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2899 2.76 - 3.29: 18804 3.29 - 3.83: 43771 3.83 - 4.36: 53391 4.36 - 4.90: 81949 Nonbonded interactions: 200814 Sorted by model distance: nonbonded pdb=" OE1 GLU15 105 " pdb=" NB CLA15 302 " model vdw 2.224 3.120 nonbonded pdb=" OE1 GLU13 73 " pdb=" NC CLA13 307 " model vdw 2.230 3.120 nonbonded pdb=" OH TYR11 98 " pdb=" O LEU16 122 " model vdw 2.252 3.040 nonbonded pdb=" O PRO 8 80 " pdb=" OH TYR 8 99 " model vdw 2.256 3.040 nonbonded pdb=" OE2 GLU12 134 " pdb=" OH TYR12 140 " model vdw 2.261 3.040 ... (remaining 200809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 12.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.100 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.044 0.871 25454 Z= 2.358 Angle : 3.936 47.490 36557 Z= 1.344 Chirality : 0.243 1.797 2923 Planarity : 0.056 0.571 4475 Dihedral : 31.530 179.525 10599 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.99 % Favored : 91.84 % Rotamer: Outliers : 0.27 % Allowed : 4.78 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.64 % Twisted Proline : 0.77 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.26 (0.14), residues: 1827 helix: -3.99 (0.08), residues: 973 sheet: None (None), residues: 0 loop : -2.76 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG12 176 TYR 0.040 0.002 TYR10 149 PHE 0.028 0.002 PHE 6 191 TRP 0.025 0.002 TRP14 138 HIS 0.037 0.003 HIS12 139 Details of bonding type rmsd/Z covalent geometry : bond 0.04128 / 2.06 (25316) covalent geometry : angle 3.93567 / 1.34 (36557) hydrogen bonds : bond 0.27539 / 18.17 ( 718) hydrogen bonds : angle 9.84014 / 6.85 ( 2097) Misc. bond : bond 0.21698 / 13.61 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 297 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 210 MET cc_start: 0.8098 (mmm) cc_final: 0.7880 (mmm) REVERT: 7 216 MET cc_start: 0.8566 (mtm) cc_final: 0.8298 (mtp) REVERT: 7 227 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6343 (mm-30) REVERT: 7 266 MET cc_start: 0.8887 (mtm) cc_final: 0.8497 (mtm) REVERT: 11 80 MET cc_start: 0.9202 (mtm) cc_final: 0.8981 (mtm) REVERT: 11 189 ASP cc_start: 0.7724 (p0) cc_final: 0.7444 (p0) REVERT: 12 49 ASN cc_start: 0.8285 (t0) cc_final: 0.7892 (t0) REVERT: 12 52 ASP cc_start: 0.8259 (m-30) cc_final: 0.8048 (m-30) REVERT: 13 222 MET cc_start: 0.8373 (mtm) cc_final: 0.8148 (mtp) REVERT: 14 92 MET cc_start: 0.8679 (mtm) cc_final: 0.8303 (mtm) REVERT: 14 127 GLU cc_start: 0.7946 (mp0) cc_final: 0.7556 (mp0) REVERT: 14 159 MET cc_start: 0.9081 (mtp) cc_final: 0.8808 (mtt) REVERT: 15 78 TYR cc_start: 0.7822 (t80) cc_final: 0.7388 (t80) REVERT: 15 92 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7859 (mttm) REVERT: 15 102 ARG cc_start: 0.8465 (mtp180) cc_final: 0.8132 (mtp85) REVERT: 15 131 GLN cc_start: 0.7456 (tp-100) cc_final: 0.7073 (tm-30) REVERT: 15 137 PRO cc_start: 0.5460 (Cg_endo) cc_final: 0.5091 (Cg_exo) REVERT: 15 146 GLU cc_start: 0.7281 (pp20) cc_final: 0.7074 (pp20) REVERT: 15 187 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7584 (ttpp) REVERT: 15 215 LYS cc_start: 0.7834 (mppt) cc_final: 0.7434 (mmtm) REVERT: 15 223 GLU cc_start: 0.7528 (pm20) cc_final: 0.7201 (pm20) REVERT: 15 237 MET cc_start: 0.7855 (mtt) cc_final: 0.7630 (ttm) REVERT: 16 88 MET cc_start: 0.8586 (mtm) cc_final: 0.8293 (mtm) outliers start: 4 outliers final: 5 residues processed: 301 average time/residue: 0.7088 time to fit residues: 241.6985 Evaluate side-chains 234 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 229 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 14 residue 42 ASP Chi-restraints excluded: chain 15 residue 138 HIS Chi-restraints excluded: chain 15 residue 253 VAL Chi-restraints excluded: chain 16 residue 168 ILE Chi-restraints excluded: chain 16 residue 209 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 171 GLN 7 189 GLN 8 112 GLN 10 201 HIS 11 61 GLN 11 94 HIS 11 105 ASN 12 200 ASN 14 82 GLN 14 106 HIS 14 169 ASN 14 183 ASN 15 94 ASN ** 15 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 190 GLN 15 200 ASN 16 177 GLN 16 182 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.107164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078580 restraints weight = 49229.628| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.48 r_work: 0.3029 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.578 25454 Z= 0.226 Angle : 1.182 43.433 36557 Z= 0.450 Chirality : 0.052 0.807 2923 Planarity : 0.006 0.054 4475 Dihedral : 27.805 179.068 7301 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.06 % Favored : 92.72 % Rotamer: Outliers : 1.84 % Allowed : 12.42 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.64 % Twisted Proline : 0.77 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.17), residues: 1827 helix: -1.27 (0.14), residues: 991 sheet: None (None), residues: 0 loop : -2.27 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG13 76 TYR 0.034 0.002 TYR14 185 PHE 0.024 0.001 PHE14 146 TRP 0.015 0.001 TRP 6 130 HIS 0.008 0.002 HIS 6 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (25316) covalent geometry : angle 1.18190 / 0.45 (36557) hydrogen bonds : bond 0.05789 / 3.77 ( 718) hydrogen bonds : angle 4.65344 / 3.23 ( 2097) Misc. bond : bond 0.17109 / 10.16 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 210 MET cc_start: 0.8958 (mmm) cc_final: 0.8709 (mmm) REVERT: 7 227 GLU cc_start: 0.7860 (mt-10) cc_final: 0.6594 (mm-30) REVERT: 7 285 GLU cc_start: 0.8908 (pt0) cc_final: 0.8601 (pt0) REVERT: 10 112 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8227 (mtpp) REVERT: 11 105 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8396 (p0) REVERT: 12 49 ASN cc_start: 0.8876 (t0) cc_final: 0.8548 (t0) REVERT: 12 52 ASP cc_start: 0.8934 (m-30) cc_final: 0.8606 (m-30) REVERT: 12 57 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8542 (mt-10) REVERT: 12 160 ASP cc_start: 0.7565 (t0) cc_final: 0.7346 (t0) REVERT: 13 76 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.7814 (mtt-85) REVERT: 13 220 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8512 (tt) REVERT: 14 58 TYR cc_start: 0.8576 (t80) cc_final: 0.8314 (t80) REVERT: 14 92 MET cc_start: 0.8695 (mtm) cc_final: 0.8429 (mtm) REVERT: 14 109 TRP cc_start: 0.6469 (p90) cc_final: 0.5549 (p-90) REVERT: 14 127 GLU cc_start: 0.7916 (mp0) cc_final: 0.7632 (mp0) REVERT: 14 159 MET cc_start: 0.9183 (mtp) cc_final: 0.8918 (mtt) REVERT: 14 214 MET cc_start: 0.8447 (mtm) cc_final: 0.8064 (mtt) REVERT: 15 66 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6790 (mp0) REVERT: 15 70 LYS cc_start: 0.7774 (mmmt) cc_final: 0.7486 (mmtt) REVERT: 15 137 PRO cc_start: 0.6075 (Cg_endo) cc_final: 0.5677 (Cg_exo) REVERT: 15 187 LYS cc_start: 0.7520 (ttpp) cc_final: 0.6950 (ttpp) REVERT: 15 190 GLN cc_start: 0.8339 (tt0) cc_final: 0.8072 (tt0) REVERT: 15 215 LYS cc_start: 0.7599 (mppt) cc_final: 0.7135 (mmtm) REVERT: 15 237 MET cc_start: 0.6828 (mtt) cc_final: 0.6416 (mtm) REVERT: 15 245 CYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6742 (t) REVERT: 16 88 MET cc_start: 0.8920 (mtm) cc_final: 0.8630 (mtm) outliers start: 27 outliers final: 8 residues processed: 265 average time/residue: 0.7111 time to fit residues: 215.1001 Evaluate side-chains 236 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 224 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 36 LYS Chi-restraints excluded: chain 10 residue 112 LYS Chi-restraints excluded: chain 11 residue 105 ASN Chi-restraints excluded: chain 13 residue 220 LEU Chi-restraints excluded: chain 14 residue 42 ASP Chi-restraints excluded: chain 15 residue 121 VAL Chi-restraints excluded: chain 15 residue 138 HIS Chi-restraints excluded: chain 15 residue 245 CYS Chi-restraints excluded: chain 15 residue 248 THR Chi-restraints excluded: chain 15 residue 253 VAL Chi-restraints excluded: chain 15 residue 272 GLU Chi-restraints excluded: chain 16 residue 209 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 114 optimal weight: 0.3980 chunk 137 optimal weight: 0.2980 chunk 57 optimal weight: 0.3980 chunk 133 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 chunk 125 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 8 167 ASN 11 105 ASN 12 200 ASN ** 13 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 14 169 ASN 14 209 ASN ** 15 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.107943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.079402 restraints weight = 49062.139| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.48 r_work: 0.3035 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.480 25454 Z= 0.946 Angle : 1.094 43.882 36557 Z= 0.416 Chirality : 0.049 0.813 2923 Planarity : 0.005 0.053 4475 Dihedral : 26.824 179.560 7299 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.61 % Favored : 92.23 % Rotamer: Outliers : 2.66 % Allowed : 13.31 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.64 % Twisted Proline : 0.77 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.19), residues: 1827 helix: -0.17 (0.15), residues: 991 sheet: None (None), residues: 0 loop : -1.91 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG15 225 TYR 0.024 0.002 TYR14 185 PHE 0.020 0.001 PHE14 146 TRP 0.014 0.001 TRP 6 130 HIS 0.007 0.002 HIS 6 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (25316) covalent geometry : angle 1.09382 / 0.42 (36557) hydrogen bonds : bond 0.05058 / 3.28 ( 718) hydrogen bonds : angle 4.32493 / 3.01 ( 2097) Misc. bond : bond 0.21084 / 13.36 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 100 TYR cc_start: 0.8412 (t80) cc_final: 0.8162 (t80) REVERT: 6 208 VAL cc_start: 0.7265 (OUTLIER) cc_final: 0.6609 (p) REVERT: 7 210 MET cc_start: 0.8925 (mmm) cc_final: 0.8682 (mmm) REVERT: 7 224 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: 7 227 GLU cc_start: 0.7878 (mt-10) cc_final: 0.6640 (mm-30) REVERT: 7 285 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8565 (pt0) REVERT: 11 115 TRP cc_start: 0.8818 (OUTLIER) cc_final: 0.8337 (m-10) REVERT: 12 49 ASN cc_start: 0.8808 (t0) cc_final: 0.8478 (t0) REVERT: 12 52 ASP cc_start: 0.8939 (m-30) cc_final: 0.8590 (m-30) REVERT: 12 57 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8600 (mt-10) REVERT: 13 76 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.7779 (mtt-85) REVERT: 13 144 ASP cc_start: 0.8270 (m-30) cc_final: 0.7934 (m-30) REVERT: 13 220 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8359 (tt) REVERT: 14 58 TYR cc_start: 0.8568 (t80) cc_final: 0.8320 (t80) REVERT: 14 109 TRP cc_start: 0.6442 (p90) cc_final: 0.5625 (p-90) REVERT: 14 111 MET cc_start: 0.5533 (tpt) cc_final: 0.5140 (tpp) REVERT: 14 127 GLU cc_start: 0.8050 (mp0) cc_final: 0.7637 (mp0) REVERT: 14 142 LEU cc_start: 0.9064 (mt) cc_final: 0.8854 (mt) REVERT: 14 159 MET cc_start: 0.9200 (mtp) cc_final: 0.8937 (mtt) REVERT: 14 192 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6334 (pmmt) REVERT: 15 70 LYS cc_start: 0.7861 (mmmt) cc_final: 0.7629 (mmtt) REVERT: 15 78 TYR cc_start: 0.7648 (t80) cc_final: 0.7401 (t80) REVERT: 15 137 PRO cc_start: 0.5916 (Cg_endo) cc_final: 0.5501 (Cg_exo) REVERT: 15 187 LYS cc_start: 0.7345 (ttpp) cc_final: 0.6840 (ttpp) REVERT: 15 190 GLN cc_start: 0.8260 (tt0) cc_final: 0.8005 (tt0) REVERT: 15 237 MET cc_start: 0.6679 (mtt) cc_final: 0.6208 (mtm) REVERT: 15 245 CYS cc_start: 0.7308 (m) cc_final: 0.6933 (t) REVERT: 16 88 MET cc_start: 0.8926 (mtm) cc_final: 0.8593 (mtm) outliers start: 39 outliers final: 15 residues processed: 263 average time/residue: 0.7005 time to fit residues: 210.3517 Evaluate side-chains 245 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 36 LYS Chi-restraints excluded: chain 6 residue 113 THR Chi-restraints excluded: chain 6 residue 208 VAL Chi-restraints excluded: chain 7 residue 224 GLN Chi-restraints excluded: chain 7 residue 285 GLU Chi-restraints excluded: chain 11 residue 115 TRP Chi-restraints excluded: chain 13 residue 220 LEU Chi-restraints excluded: chain 14 residue 42 ASP Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 192 LYS Chi-restraints excluded: chain 14 residue 203 LEU Chi-restraints excluded: chain 14 residue 226 VAL Chi-restraints excluded: chain 15 residue 97 THR Chi-restraints excluded: chain 15 residue 121 VAL Chi-restraints excluded: chain 15 residue 138 HIS Chi-restraints excluded: chain 15 residue 238 LEU Chi-restraints excluded: chain 15 residue 248 THR Chi-restraints excluded: chain 15 residue 253 VAL Chi-restraints excluded: chain 15 residue 272 GLU Chi-restraints excluded: chain 16 residue 148 GLU Chi-restraints excluded: chain 16 residue 209 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 176 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 8 167 ASN 12 200 ASN ** 13 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 14 169 ASN 14 198 GLN 15 214 ASN ** 15 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 182 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.107475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.078841 restraints weight = 49316.756| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.48 r_work: 0.3033 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 1.173 25454 Z= 0.212 Angle : 1.088 44.101 36557 Z= 0.415 Chirality : 0.049 0.819 2923 Planarity : 0.005 0.045 4475 Dihedral : 26.395 179.320 7299 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.33 % Favored : 92.45 % Rotamer: Outliers : 2.53 % Allowed : 14.88 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.64 % Twisted Proline : 0.77 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.19), residues: 1827 helix: 0.28 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -1.74 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG13 76 TYR 0.024 0.002 TYR14 240 PHE 0.020 0.001 PHE 6 191 TRP 0.014 0.001 TRP 6 130 HIS 0.007 0.002 HIS 6 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (25316) covalent geometry : angle 1.08833 / 0.41 (36557) hydrogen bonds : bond 0.04959 / 3.22 ( 718) hydrogen bonds : angle 4.20745 / 2.93 ( 2097) Misc. bond : bond 0.18978 / 12.73 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 100 TYR cc_start: 0.8463 (t80) cc_final: 0.8227 (t80) REVERT: 6 170 GLU cc_start: 0.8032 (pp20) cc_final: 0.7829 (pp20) REVERT: 7 210 MET cc_start: 0.8928 (mmm) cc_final: 0.8688 (mmm) REVERT: 7 227 GLU cc_start: 0.7780 (mt-10) cc_final: 0.6535 (mm-30) REVERT: 7 285 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8561 (pt0) REVERT: 11 115 TRP cc_start: 0.8848 (OUTLIER) cc_final: 0.8378 (m-10) REVERT: 11 185 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7221 (mm-30) REVERT: 12 49 ASN cc_start: 0.8791 (t0) cc_final: 0.8425 (t0) REVERT: 12 52 ASP cc_start: 0.8920 (m-30) cc_final: 0.8551 (m-30) REVERT: 12 57 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8684 (mt-10) REVERT: 13 76 ARG cc_start: 0.8433 (mtm-85) cc_final: 0.7758 (mtt-85) REVERT: 13 144 ASP cc_start: 0.8246 (m-30) cc_final: 0.7895 (m-30) REVERT: 13 220 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8361 (tt) REVERT: 14 58 TYR cc_start: 0.8530 (t80) cc_final: 0.8262 (t80) REVERT: 14 109 TRP cc_start: 0.6422 (p90) cc_final: 0.5631 (p-90) REVERT: 14 111 MET cc_start: 0.5630 (tpt) cc_final: 0.5240 (tpp) REVERT: 14 127 GLU cc_start: 0.8076 (mp0) cc_final: 0.7633 (mp0) REVERT: 14 142 LEU cc_start: 0.9058 (mt) cc_final: 0.8844 (mt) REVERT: 14 159 MET cc_start: 0.9216 (mtp) cc_final: 0.8944 (mtt) REVERT: 15 70 LYS cc_start: 0.8062 (mmmt) cc_final: 0.7776 (mmtt) REVERT: 15 137 PRO cc_start: 0.5836 (Cg_endo) cc_final: 0.5402 (Cg_exo) REVERT: 15 187 LYS cc_start: 0.7313 (ttpp) cc_final: 0.6883 (ttpp) REVERT: 15 217 MET cc_start: 0.3125 (ptp) cc_final: 0.2602 (ptt) REVERT: 15 237 MET cc_start: 0.6700 (mtt) cc_final: 0.6232 (mtm) REVERT: 15 245 CYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6948 (t) REVERT: 16 88 MET cc_start: 0.8922 (mtm) cc_final: 0.8612 (mtm) outliers start: 37 outliers final: 17 residues processed: 254 average time/residue: 0.6966 time to fit residues: 202.5448 Evaluate side-chains 237 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 36 LYS Chi-restraints excluded: chain 6 residue 113 THR Chi-restraints excluded: chain 6 residue 194 VAL Chi-restraints excluded: chain 7 residue 285 GLU Chi-restraints excluded: chain 8 residue 76 VAL Chi-restraints excluded: chain 8 residue 187 LEU Chi-restraints excluded: chain 11 residue 115 TRP Chi-restraints excluded: chain 13 residue 220 LEU Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 203 LEU Chi-restraints excluded: chain 14 residue 226 VAL Chi-restraints excluded: chain 15 residue 97 THR Chi-restraints excluded: chain 15 residue 121 VAL Chi-restraints excluded: chain 15 residue 138 HIS Chi-restraints excluded: chain 15 residue 238 LEU Chi-restraints excluded: chain 15 residue 245 CYS Chi-restraints excluded: chain 15 residue 248 THR Chi-restraints excluded: chain 15 residue 253 VAL Chi-restraints excluded: chain 15 residue 272 GLU Chi-restraints excluded: chain 16 residue 148 GLU Chi-restraints excluded: chain 16 residue 209 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 77 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 149 optimal weight: 30.0000 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 120 GLN 8 167 ASN 12 200 ASN ** 13 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 14 169 ASN ** 14 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 209 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.106984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.078299 restraints weight = 48939.770| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.47 r_work: 0.3023 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 2.026 25454 Z= 1.289 Angle : 1.091 44.188 36557 Z= 0.416 Chirality : 0.050 0.814 2923 Planarity : 0.005 0.059 4475 Dihedral : 26.177 178.848 7297 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.72 % Favored : 92.12 % Rotamer: Outliers : 2.39 % Allowed : 15.63 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.64 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.20), residues: 1827 helix: 0.43 (0.16), residues: 997 sheet: None (None), residues: 0 loop : -1.66 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG15 225 TYR 0.025 0.002 TYR14 240 PHE 0.019 0.001 PHE 6 191 TRP 0.013 0.001 TRP 6 130 HIS 0.007 0.002 HIS 7 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (25316) covalent geometry : angle 1.09122 / 0.42 (36557) hydrogen bonds : bond 0.04948 / 3.22 ( 718) hydrogen bonds : angle 4.20053 / 2.93 ( 2097) Misc. bond : bond 0.25093 / 16.23 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 100 TYR cc_start: 0.8455 (t80) cc_final: 0.8238 (t80) REVERT: 7 210 MET cc_start: 0.8901 (mmm) cc_final: 0.8672 (mmm) REVERT: 7 227 GLU cc_start: 0.7758 (mt-10) cc_final: 0.6500 (mm-30) REVERT: 7 285 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8568 (pt0) REVERT: 10 112 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8308 (mtpp) REVERT: 11 115 TRP cc_start: 0.8858 (OUTLIER) cc_final: 0.8396 (m-10) REVERT: 11 135 ASP cc_start: 0.9031 (m-30) cc_final: 0.8742 (m-30) REVERT: 11 185 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7231 (mm-30) REVERT: 12 49 ASN cc_start: 0.8796 (t0) cc_final: 0.8430 (t0) REVERT: 12 52 ASP cc_start: 0.8930 (m-30) cc_final: 0.8558 (m-30) REVERT: 12 149 MET cc_start: 0.9199 (ttm) cc_final: 0.8967 (ttp) REVERT: 12 155 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8182 (t0) REVERT: 13 76 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.7754 (mtt-85) REVERT: 13 144 ASP cc_start: 0.8254 (m-30) cc_final: 0.7895 (m-30) REVERT: 13 220 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8387 (tt) REVERT: 14 58 TYR cc_start: 0.8534 (t80) cc_final: 0.8262 (t80) REVERT: 14 109 TRP cc_start: 0.6453 (p90) cc_final: 0.5662 (p-90) REVERT: 14 111 MET cc_start: 0.5638 (tpt) cc_final: 0.5254 (tpp) REVERT: 14 127 GLU cc_start: 0.8153 (mp0) cc_final: 0.7698 (mp0) REVERT: 14 142 LEU cc_start: 0.9056 (mt) cc_final: 0.8834 (mt) REVERT: 14 159 MET cc_start: 0.9218 (mtp) cc_final: 0.8935 (mtt) REVERT: 15 70 LYS cc_start: 0.8017 (mmmt) cc_final: 0.7722 (mmtt) REVERT: 15 137 PRO cc_start: 0.5896 (Cg_endo) cc_final: 0.5458 (Cg_exo) REVERT: 15 187 LYS cc_start: 0.7291 (ttpp) cc_final: 0.6923 (ttpp) REVERT: 15 217 MET cc_start: 0.3097 (ptp) cc_final: 0.2517 (ptt) REVERT: 15 224 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6488 (tmt170) REVERT: 15 237 MET cc_start: 0.6709 (mtt) cc_final: 0.6220 (mtm) REVERT: 15 245 CYS cc_start: 0.7331 (OUTLIER) cc_final: 0.7001 (t) REVERT: 16 88 MET cc_start: 0.8886 (mtm) cc_final: 0.8570 (mtm) outliers start: 35 outliers final: 21 residues processed: 245 average time/residue: 0.7084 time to fit residues: 198.1578 Evaluate side-chains 243 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 36 LYS Chi-restraints excluded: chain 6 residue 113 THR Chi-restraints excluded: chain 6 residue 125 SER Chi-restraints excluded: chain 6 residue 175 GLU Chi-restraints excluded: chain 6 residue 194 VAL Chi-restraints excluded: chain 7 residue 124 ASP Chi-restraints excluded: chain 7 residue 285 GLU Chi-restraints excluded: chain 8 residue 58 MET Chi-restraints excluded: chain 8 residue 76 VAL Chi-restraints excluded: chain 8 residue 187 LEU Chi-restraints excluded: chain 10 residue 112 LYS Chi-restraints excluded: chain 11 residue 52 LEU Chi-restraints excluded: chain 11 residue 115 TRP Chi-restraints excluded: chain 12 residue 155 ASP Chi-restraints excluded: chain 13 residue 220 LEU Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 226 VAL Chi-restraints excluded: chain 15 residue 97 THR Chi-restraints excluded: chain 15 residue 121 VAL Chi-restraints excluded: chain 15 residue 138 HIS Chi-restraints excluded: chain 15 residue 224 ARG Chi-restraints excluded: chain 15 residue 238 LEU Chi-restraints excluded: chain 15 residue 245 CYS Chi-restraints excluded: chain 15 residue 248 THR Chi-restraints excluded: chain 15 residue 253 VAL Chi-restraints excluded: chain 15 residue 272 GLU Chi-restraints excluded: chain 16 residue 148 GLU Chi-restraints excluded: chain 16 residue 209 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 64 optimal weight: 0.3980 chunk 87 optimal weight: 0.7980 chunk 10 optimal weight: 0.0770 chunk 44 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 120 GLN 8 167 ASN 12 200 ASN ** 13 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 182 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.107068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.078357 restraints weight = 49086.968| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.48 r_work: 0.3023 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 1.980 25454 Z= 1.264 Angle : 1.092 44.188 36557 Z= 0.417 Chirality : 0.050 0.814 2923 Planarity : 0.005 0.059 4475 Dihedral : 26.251 178.848 7297 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.72 % Favored : 92.12 % Rotamer: Outliers : 1.98 % Allowed : 16.25 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.64 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.20), residues: 1827 helix: 0.43 (0.16), residues: 997 sheet: None (None), residues: 0 loop : -1.66 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG15 225 TYR 0.025 0.002 TYR14 240 PHE 0.019 0.001 PHE 6 191 TRP 0.013 0.001 TRP 6 130 HIS 0.007 0.002 HIS 7 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (25316) covalent geometry : angle 1.09173 / 0.42 (36557) hydrogen bonds : bond 0.04948 / 3.22 ( 718) hydrogen bonds : angle 4.20054 / 2.93 ( 2097) Misc. bond : bond 0.27333 / 18.39 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 100 TYR cc_start: 0.8457 (t80) cc_final: 0.8247 (t80) REVERT: 7 210 MET cc_start: 0.8904 (mmm) cc_final: 0.8691 (mmm) REVERT: 7 227 GLU cc_start: 0.7774 (mt-10) cc_final: 0.6541 (mm-30) REVERT: 7 285 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8573 (pt0) REVERT: 10 112 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8311 (mtpp) REVERT: 11 115 TRP cc_start: 0.8868 (OUTLIER) cc_final: 0.8403 (m-10) REVERT: 11 135 ASP cc_start: 0.9035 (m-30) cc_final: 0.8746 (m-30) REVERT: 11 185 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7236 (mm-30) REVERT: 12 49 ASN cc_start: 0.8800 (t0) cc_final: 0.8436 (t0) REVERT: 12 52 ASP cc_start: 0.8927 (m-30) cc_final: 0.8566 (m-30) REVERT: 12 149 MET cc_start: 0.9200 (ttm) cc_final: 0.8973 (ttp) REVERT: 12 155 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8208 (t0) REVERT: 13 76 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.7785 (mtt-85) REVERT: 13 144 ASP cc_start: 0.8256 (m-30) cc_final: 0.7896 (m-30) REVERT: 13 220 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8416 (tt) REVERT: 14 58 TYR cc_start: 0.8560 (t80) cc_final: 0.8290 (t80) REVERT: 14 109 TRP cc_start: 0.6450 (p90) cc_final: 0.5662 (p-90) REVERT: 14 111 MET cc_start: 0.5662 (tpt) cc_final: 0.5273 (tpp) REVERT: 14 127 GLU cc_start: 0.8144 (mp0) cc_final: 0.7708 (mp0) REVERT: 14 142 LEU cc_start: 0.9086 (mt) cc_final: 0.8863 (mt) REVERT: 14 159 MET cc_start: 0.9224 (mtp) cc_final: 0.8935 (mtt) REVERT: 15 70 LYS cc_start: 0.8019 (mmmt) cc_final: 0.7720 (mmtt) REVERT: 15 137 PRO cc_start: 0.5904 (Cg_endo) cc_final: 0.5467 (Cg_exo) REVERT: 15 187 LYS cc_start: 0.7326 (ttpp) cc_final: 0.6968 (ttpp) REVERT: 15 217 MET cc_start: 0.3010 (ptp) cc_final: 0.2508 (ptt) REVERT: 15 237 MET cc_start: 0.6787 (mtt) cc_final: 0.6289 (mtm) REVERT: 15 245 CYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6992 (t) REVERT: 16 88 MET cc_start: 0.8895 (mtm) cc_final: 0.8589 (mtm) outliers start: 29 outliers final: 21 residues processed: 232 average time/residue: 0.7222 time to fit residues: 191.1909 Evaluate side-chains 241 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 36 LYS Chi-restraints excluded: chain 6 residue 113 THR Chi-restraints excluded: chain 6 residue 125 SER Chi-restraints excluded: chain 6 residue 175 GLU Chi-restraints excluded: chain 6 residue 194 VAL Chi-restraints excluded: chain 7 residue 124 ASP Chi-restraints excluded: chain 7 residue 285 GLU Chi-restraints excluded: chain 8 residue 58 MET Chi-restraints excluded: chain 8 residue 76 VAL Chi-restraints excluded: chain 8 residue 187 LEU Chi-restraints excluded: chain 10 residue 112 LYS Chi-restraints excluded: chain 11 residue 52 LEU Chi-restraints excluded: chain 11 residue 115 TRP Chi-restraints excluded: chain 12 residue 155 ASP Chi-restraints excluded: chain 13 residue 220 LEU Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 226 VAL Chi-restraints excluded: chain 15 residue 97 THR Chi-restraints excluded: chain 15 residue 121 VAL Chi-restraints excluded: chain 15 residue 138 HIS Chi-restraints excluded: chain 15 residue 238 LEU Chi-restraints excluded: chain 15 residue 245 CYS Chi-restraints excluded: chain 15 residue 248 THR Chi-restraints excluded: chain 15 residue 253 VAL Chi-restraints excluded: chain 15 residue 272 GLU Chi-restraints excluded: chain 16 residue 148 GLU Chi-restraints excluded: chain 16 residue 209 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 28 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 96 optimal weight: 0.2980 chunk 109 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 26 optimal weight: 0.0370 chunk 31 optimal weight: 0.9980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 120 GLN 12 200 ASN ** 13 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.107600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.079037 restraints weight = 48773.745| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.47 r_work: 0.3040 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 1.112 25454 Z= 0.197 Angle : 1.078 44.054 36557 Z= 0.412 Chirality : 0.049 0.832 2923 Planarity : 0.005 0.042 4475 Dihedral : 26.181 178.699 7297 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.66 % Favored : 92.12 % Rotamer: Outliers : 2.66 % Allowed : 15.84 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.64 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.20), residues: 1827 helix: 0.54 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -1.62 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG14 211 TYR 0.025 0.001 TYR14 240 PHE 0.017 0.001 PHE 6 191 TRP 0.013 0.001 TRP 6 130 HIS 0.006 0.002 HIS 6 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (25316) covalent geometry : angle 1.07834 / 0.41 (36557) hydrogen bonds : bond 0.04857 / 3.17 ( 718) hydrogen bonds : angle 4.19102 / 2.92 ( 2097) Misc. bond : bond 0.18884 / 12.81 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 100 TYR cc_start: 0.8354 (t80) cc_final: 0.8132 (t80) REVERT: 7 210 MET cc_start: 0.8902 (mmm) cc_final: 0.8679 (mmm) REVERT: 7 227 GLU cc_start: 0.7681 (mt-10) cc_final: 0.6406 (mm-30) REVERT: 7 285 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8560 (pt0) REVERT: 8 127 MET cc_start: 0.9506 (mmt) cc_final: 0.9261 (mmp) REVERT: 10 112 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8294 (mtpp) REVERT: 11 115 TRP cc_start: 0.8849 (OUTLIER) cc_final: 0.8443 (m-10) REVERT: 11 135 ASP cc_start: 0.9013 (m-30) cc_final: 0.8723 (m-30) REVERT: 11 185 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7223 (mm-30) REVERT: 12 49 ASN cc_start: 0.8783 (t0) cc_final: 0.8415 (t0) REVERT: 12 52 ASP cc_start: 0.8922 (m-30) cc_final: 0.8544 (m-30) REVERT: 12 149 MET cc_start: 0.9213 (ttm) cc_final: 0.8981 (ttp) REVERT: 12 155 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8161 (t0) REVERT: 13 144 ASP cc_start: 0.8223 (m-30) cc_final: 0.7849 (m-30) REVERT: 13 220 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8355 (tt) REVERT: 14 58 TYR cc_start: 0.8515 (t80) cc_final: 0.8261 (t80) REVERT: 14 109 TRP cc_start: 0.6426 (p90) cc_final: 0.5661 (p-90) REVERT: 14 111 MET cc_start: 0.5640 (tpt) cc_final: 0.5265 (tpp) REVERT: 14 127 GLU cc_start: 0.8187 (mp0) cc_final: 0.7731 (mp0) REVERT: 14 142 LEU cc_start: 0.9055 (mt) cc_final: 0.8723 (mm) REVERT: 14 159 MET cc_start: 0.9214 (mtp) cc_final: 0.8910 (mtt) REVERT: 15 137 PRO cc_start: 0.5854 (Cg_endo) cc_final: 0.5412 (Cg_exo) REVERT: 15 187 LYS cc_start: 0.7277 (ttpp) cc_final: 0.6884 (ttpp) REVERT: 15 217 MET cc_start: 0.3025 (ptp) cc_final: 0.2564 (ptt) REVERT: 15 237 MET cc_start: 0.6735 (mtt) cc_final: 0.6295 (mtm) REVERT: 15 245 CYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6997 (t) REVERT: 16 88 MET cc_start: 0.8901 (mtm) cc_final: 0.8590 (mtm) outliers start: 39 outliers final: 20 residues processed: 247 average time/residue: 0.7157 time to fit residues: 201.2320 Evaluate side-chains 241 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 36 LYS Chi-restraints excluded: chain 6 residue 113 THR Chi-restraints excluded: chain 6 residue 175 GLU Chi-restraints excluded: chain 6 residue 194 VAL Chi-restraints excluded: chain 7 residue 124 ASP Chi-restraints excluded: chain 7 residue 285 GLU Chi-restraints excluded: chain 8 residue 76 VAL Chi-restraints excluded: chain 8 residue 187 LEU Chi-restraints excluded: chain 10 residue 112 LYS Chi-restraints excluded: chain 11 residue 52 LEU Chi-restraints excluded: chain 11 residue 115 TRP Chi-restraints excluded: chain 12 residue 57 GLU Chi-restraints excluded: chain 12 residue 155 ASP Chi-restraints excluded: chain 13 residue 220 LEU Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 226 VAL Chi-restraints excluded: chain 15 residue 97 THR Chi-restraints excluded: chain 15 residue 121 VAL Chi-restraints excluded: chain 15 residue 138 HIS Chi-restraints excluded: chain 15 residue 245 CYS Chi-restraints excluded: chain 15 residue 248 THR Chi-restraints excluded: chain 15 residue 253 VAL Chi-restraints excluded: chain 15 residue 271 PHE Chi-restraints excluded: chain 15 residue 272 GLU Chi-restraints excluded: chain 16 residue 148 GLU Chi-restraints excluded: chain 16 residue 209 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 106 optimal weight: 0.6980 chunk 116 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 73 optimal weight: 0.0970 chunk 24 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 131 optimal weight: 0.0980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 120 GLN 8 167 ASN 12 200 ASN 14 209 ASN ** 15 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.108139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079596 restraints weight = 48890.947| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.49 r_work: 0.3043 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 2.120 25454 Z= 1.341 Angle : 1.057 43.907 36557 Z= 0.404 Chirality : 0.048 0.832 2923 Planarity : 0.005 0.058 4475 Dihedral : 25.773 177.617 7297 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.61 % Favored : 92.23 % Rotamer: Outliers : 1.91 % Allowed : 16.59 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.64 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1827 helix: 0.70 (0.16), residues: 989 sheet: None (None), residues: 0 loop : -1.54 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG13 76 TYR 0.029 0.001 TYR14 240 PHE 0.016 0.001 PHE 6 191 TRP 0.015 0.001 TRP14 129 HIS 0.006 0.002 HIS 6 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (25316) covalent geometry : angle 1.05655 / 0.40 (36557) hydrogen bonds : bond 0.04683 / 3.05 ( 718) hydrogen bonds : angle 4.14345 / 2.89 ( 2097) Misc. bond : bond 0.25205 / 16.30 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 100 TYR cc_start: 0.8468 (t80) cc_final: 0.8220 (t80) REVERT: 6 104 GLU cc_start: 0.8551 (mp0) cc_final: 0.8329 (mp0) REVERT: 7 153 GLU cc_start: 0.8674 (tp30) cc_final: 0.8407 (tp30) REVERT: 7 210 MET cc_start: 0.8910 (mmm) cc_final: 0.8694 (mmm) REVERT: 7 227 GLU cc_start: 0.7405 (mt-10) cc_final: 0.5991 (mm-30) REVERT: 7 285 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8595 (pt0) REVERT: 8 127 MET cc_start: 0.9487 (OUTLIER) cc_final: 0.9266 (mmp) REVERT: 10 152 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8517 (mmmm) REVERT: 11 115 TRP cc_start: 0.8866 (OUTLIER) cc_final: 0.8483 (m-10) REVERT: 11 135 ASP cc_start: 0.8991 (m-30) cc_final: 0.8677 (m-30) REVERT: 11 185 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7221 (mm-30) REVERT: 12 49 ASN cc_start: 0.8791 (t0) cc_final: 0.8426 (t0) REVERT: 12 52 ASP cc_start: 0.8934 (m-30) cc_final: 0.8555 (m-30) REVERT: 12 149 MET cc_start: 0.9238 (ttm) cc_final: 0.9011 (ttp) REVERT: 12 155 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8148 (t0) REVERT: 13 76 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.7661 (mtt-85) REVERT: 13 141 GLU cc_start: 0.7462 (pm20) cc_final: 0.7238 (pm20) REVERT: 13 144 ASP cc_start: 0.8191 (m-30) cc_final: 0.7828 (m-30) REVERT: 13 220 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8338 (tt) REVERT: 13 222 MET cc_start: 0.8154 (mtm) cc_final: 0.7925 (mtm) REVERT: 14 58 TYR cc_start: 0.8572 (t80) cc_final: 0.8334 (t80) REVERT: 14 109 TRP cc_start: 0.6343 (p90) cc_final: 0.5666 (p-90) REVERT: 14 111 MET cc_start: 0.5900 (tpt) cc_final: 0.4932 (tpp) REVERT: 14 127 GLU cc_start: 0.8163 (mp0) cc_final: 0.7723 (mp0) REVERT: 14 142 LEU cc_start: 0.9044 (mt) cc_final: 0.8701 (mm) REVERT: 14 159 MET cc_start: 0.9206 (mtp) cc_final: 0.8905 (mtt) REVERT: 15 137 PRO cc_start: 0.5869 (Cg_endo) cc_final: 0.5418 (Cg_exo) REVERT: 15 187 LYS cc_start: 0.7224 (ttpp) cc_final: 0.6762 (ttpp) REVERT: 15 190 GLN cc_start: 0.8066 (tt0) cc_final: 0.7823 (tt0) REVERT: 15 217 MET cc_start: 0.3002 (ptp) cc_final: 0.2579 (ptt) REVERT: 15 224 ARG cc_start: 0.7257 (tmt170) cc_final: 0.6976 (tmt170) REVERT: 15 237 MET cc_start: 0.6784 (mtt) cc_final: 0.6251 (mtm) REVERT: 15 245 CYS cc_start: 0.7301 (m) cc_final: 0.7016 (t) REVERT: 16 88 MET cc_start: 0.8886 (mtm) cc_final: 0.8559 (mtm) outliers start: 28 outliers final: 17 residues processed: 244 average time/residue: 0.7120 time to fit residues: 198.2643 Evaluate side-chains 241 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 219 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 36 LYS Chi-restraints excluded: chain 6 residue 113 THR Chi-restraints excluded: chain 6 residue 194 VAL Chi-restraints excluded: chain 7 residue 285 GLU Chi-restraints excluded: chain 8 residue 76 VAL Chi-restraints excluded: chain 8 residue 127 MET Chi-restraints excluded: chain 8 residue 187 LEU Chi-restraints excluded: chain 11 residue 52 LEU Chi-restraints excluded: chain 11 residue 115 TRP Chi-restraints excluded: chain 12 residue 155 ASP Chi-restraints excluded: chain 13 residue 220 LEU Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 226 VAL Chi-restraints excluded: chain 15 residue 97 THR Chi-restraints excluded: chain 15 residue 121 VAL Chi-restraints excluded: chain 15 residue 138 HIS Chi-restraints excluded: chain 15 residue 248 THR Chi-restraints excluded: chain 15 residue 253 VAL Chi-restraints excluded: chain 15 residue 271 PHE Chi-restraints excluded: chain 15 residue 272 GLU Chi-restraints excluded: chain 16 residue 148 GLU Chi-restraints excluded: chain 16 residue 209 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 81 optimal weight: 0.0770 chunk 84 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 82 optimal weight: 0.0870 chunk 45 optimal weight: 0.4980 chunk 37 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 8 167 ASN 12 200 ASN ** 15 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 232 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.108388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.079859 restraints weight = 49262.656| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.50 r_work: 0.3054 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.030 25454 Z= 0.178 Angle : 1.054 43.889 36557 Z= 0.406 Chirality : 0.048 0.836 2923 Planarity : 0.005 0.067 4475 Dihedral : 25.627 176.510 7297 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.55 % Favored : 92.23 % Rotamer: Outliers : 2.32 % Allowed : 16.52 % Favored : 81.16 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.64 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.20), residues: 1827 helix: 0.81 (0.16), residues: 991 sheet: None (None), residues: 0 loop : -1.50 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG13 76 TYR 0.026 0.001 TYR14 240 PHE 0.051 0.001 PHE15 271 TRP 0.012 0.001 TRP 6 130 HIS 0.006 0.001 HIS 6 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (25316) covalent geometry : angle 1.05445 / 0.41 (36557) hydrogen bonds : bond 0.04596 / 2.98 ( 718) hydrogen bonds : angle 4.14368 / 2.89 ( 2097) Misc. bond : bond 0.16707 / 10.62 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 100 TYR cc_start: 0.8437 (t80) cc_final: 0.8213 (t80) REVERT: 7 210 MET cc_start: 0.8902 (mmm) cc_final: 0.8654 (mmm) REVERT: 7 227 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6051 (mm-30) REVERT: 7 285 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8558 (pt0) REVERT: 8 58 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6466 (mpp) REVERT: 10 152 LYS cc_start: 0.8826 (mmmm) cc_final: 0.8502 (mmmm) REVERT: 11 115 TRP cc_start: 0.8834 (OUTLIER) cc_final: 0.8434 (m-10) REVERT: 11 135 ASP cc_start: 0.8992 (m-30) cc_final: 0.8673 (m-30) REVERT: 11 185 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7205 (mm-30) REVERT: 12 49 ASN cc_start: 0.8795 (t0) cc_final: 0.8428 (t0) REVERT: 12 52 ASP cc_start: 0.8929 (m-30) cc_final: 0.8562 (m-30) REVERT: 12 155 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8083 (t0) REVERT: 13 76 ARG cc_start: 0.8329 (mtm-85) cc_final: 0.7703 (mtt-85) REVERT: 13 144 ASP cc_start: 0.8163 (m-30) cc_final: 0.7802 (m-30) REVERT: 13 220 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8336 (tt) REVERT: 13 222 MET cc_start: 0.8269 (mtm) cc_final: 0.8041 (mtm) REVERT: 14 58 TYR cc_start: 0.8572 (t80) cc_final: 0.8325 (t80) REVERT: 14 92 MET cc_start: 0.8557 (mtm) cc_final: 0.8332 (mtm) REVERT: 14 109 TRP cc_start: 0.6309 (p90) cc_final: 0.5638 (p-90) REVERT: 14 111 MET cc_start: 0.5928 (tpt) cc_final: 0.5484 (tpp) REVERT: 14 127 GLU cc_start: 0.8153 (mp0) cc_final: 0.7702 (mp0) REVERT: 14 142 LEU cc_start: 0.9012 (mt) cc_final: 0.8734 (mm) REVERT: 14 159 MET cc_start: 0.9201 (mtp) cc_final: 0.8892 (mtt) REVERT: 14 169 ASN cc_start: 0.7852 (m-40) cc_final: 0.7005 (t0) REVERT: 15 137 PRO cc_start: 0.5888 (Cg_endo) cc_final: 0.5439 (Cg_exo) REVERT: 15 148 GLN cc_start: 0.7372 (mt0) cc_final: 0.7156 (mt0) REVERT: 15 187 LYS cc_start: 0.7215 (ttpp) cc_final: 0.6788 (ttpp) REVERT: 15 190 GLN cc_start: 0.8087 (tt0) cc_final: 0.7831 (tt0) REVERT: 15 224 ARG cc_start: 0.7386 (tmt170) cc_final: 0.7076 (tmt170) REVERT: 15 237 MET cc_start: 0.6800 (mtt) cc_final: 0.6387 (mtm) REVERT: 15 245 CYS cc_start: 0.7284 (OUTLIER) cc_final: 0.7017 (t) REVERT: 16 88 MET cc_start: 0.8854 (mtm) cc_final: 0.8517 (mtm) outliers start: 34 outliers final: 17 residues processed: 243 average time/residue: 0.7000 time to fit residues: 194.2462 Evaluate side-chains 239 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 36 LYS Chi-restraints excluded: chain 6 residue 113 THR Chi-restraints excluded: chain 6 residue 125 SER Chi-restraints excluded: chain 6 residue 194 VAL Chi-restraints excluded: chain 7 residue 285 GLU Chi-restraints excluded: chain 8 residue 58 MET Chi-restraints excluded: chain 8 residue 76 VAL Chi-restraints excluded: chain 8 residue 187 LEU Chi-restraints excluded: chain 11 residue 52 LEU Chi-restraints excluded: chain 11 residue 115 TRP Chi-restraints excluded: chain 12 residue 155 ASP Chi-restraints excluded: chain 13 residue 220 LEU Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 226 VAL Chi-restraints excluded: chain 15 residue 97 THR Chi-restraints excluded: chain 15 residue 121 VAL Chi-restraints excluded: chain 15 residue 138 HIS Chi-restraints excluded: chain 15 residue 238 LEU Chi-restraints excluded: chain 15 residue 245 CYS Chi-restraints excluded: chain 15 residue 248 THR Chi-restraints excluded: chain 15 residue 253 VAL Chi-restraints excluded: chain 16 residue 148 GLU Chi-restraints excluded: chain 16 residue 209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 126 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 8 167 ASN 12 200 ASN 14 209 ASN ** 15 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 232 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.106728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.077905 restraints weight = 49107.483| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.49 r_work: 0.3013 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 2.143 25454 Z= 1.364 Angle : 1.092 44.350 36557 Z= 0.422 Chirality : 0.050 0.829 2923 Planarity : 0.005 0.043 4475 Dihedral : 25.388 175.435 7297 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.83 % Favored : 92.01 % Rotamer: Outliers : 2.25 % Allowed : 16.79 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.64 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.20), residues: 1827 helix: 0.83 (0.16), residues: 997 sheet: None (None), residues: 0 loop : -1.46 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG13 76 TYR 0.024 0.002 TYR14 240 PHE 0.032 0.001 PHE15 271 TRP 0.012 0.001 TRP 6 130 HIS 0.007 0.002 HIS 7 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (25316) covalent geometry : angle 1.09166 / 0.42 (36557) hydrogen bonds : bond 0.04783 / 3.10 ( 718) hydrogen bonds : angle 4.16696 / 2.90 ( 2097) Misc. bond : bond 0.26523 / 16.37 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 210 MET cc_start: 0.8935 (mmm) cc_final: 0.8695 (mmm) REVERT: 7 227 GLU cc_start: 0.7276 (mt-10) cc_final: 0.5791 (mm-30) REVERT: 7 285 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8636 (pt0) REVERT: 10 152 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8536 (mmmm) REVERT: 11 115 TRP cc_start: 0.8866 (OUTLIER) cc_final: 0.8490 (m-10) REVERT: 11 135 ASP cc_start: 0.9015 (m-30) cc_final: 0.8700 (m-30) REVERT: 11 185 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7187 (mm-30) REVERT: 12 49 ASN cc_start: 0.8803 (t0) cc_final: 0.8437 (t0) REVERT: 12 52 ASP cc_start: 0.8933 (m-30) cc_final: 0.8556 (m-30) REVERT: 12 155 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8206 (t0) REVERT: 13 76 ARG cc_start: 0.8284 (mtm-85) cc_final: 0.7638 (mtt-85) REVERT: 13 144 ASP cc_start: 0.8127 (m-30) cc_final: 0.7788 (m-30) REVERT: 13 209 LYS cc_start: 0.7707 (mptt) cc_final: 0.7492 (mppt) REVERT: 13 220 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8437 (tt) REVERT: 14 58 TYR cc_start: 0.8525 (t80) cc_final: 0.8271 (t80) REVERT: 14 92 MET cc_start: 0.8558 (mtm) cc_final: 0.8275 (mtm) REVERT: 14 109 TRP cc_start: 0.6322 (p90) cc_final: 0.5663 (p-90) REVERT: 14 111 MET cc_start: 0.5805 (tpt) cc_final: 0.5386 (tpp) REVERT: 14 127 GLU cc_start: 0.8171 (mp0) cc_final: 0.7800 (mp0) REVERT: 14 142 LEU cc_start: 0.9005 (mt) cc_final: 0.8744 (mm) REVERT: 14 159 MET cc_start: 0.9203 (mtp) cc_final: 0.8902 (mtt) REVERT: 14 169 ASN cc_start: 0.7912 (m-40) cc_final: 0.7711 (t0) REVERT: 15 148 GLN cc_start: 0.7304 (mt0) cc_final: 0.6802 (mt0) REVERT: 15 190 GLN cc_start: 0.8126 (tt0) cc_final: 0.7899 (tt0) REVERT: 15 224 ARG cc_start: 0.7532 (tmt170) cc_final: 0.7054 (tmt170) REVERT: 15 237 MET cc_start: 0.6832 (mtt) cc_final: 0.6411 (mtm) REVERT: 15 245 CYS cc_start: 0.7293 (OUTLIER) cc_final: 0.7055 (t) REVERT: 16 58 LYS cc_start: 0.7889 (mmmm) cc_final: 0.7409 (tptm) REVERT: 16 88 MET cc_start: 0.8846 (mtm) cc_final: 0.8553 (mtm) outliers start: 33 outliers final: 21 residues processed: 235 average time/residue: 0.6572 time to fit residues: 177.3336 Evaluate side-chains 241 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 36 LYS Chi-restraints excluded: chain 6 residue 113 THR Chi-restraints excluded: chain 6 residue 125 SER Chi-restraints excluded: chain 6 residue 194 VAL Chi-restraints excluded: chain 7 residue 285 GLU Chi-restraints excluded: chain 8 residue 58 MET Chi-restraints excluded: chain 8 residue 76 VAL Chi-restraints excluded: chain 8 residue 187 LEU Chi-restraints excluded: chain 11 residue 52 LEU Chi-restraints excluded: chain 11 residue 115 TRP Chi-restraints excluded: chain 12 residue 155 ASP Chi-restraints excluded: chain 13 residue 220 LEU Chi-restraints excluded: chain 14 residue 42 ASP Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 209 ASN Chi-restraints excluded: chain 14 residue 226 VAL Chi-restraints excluded: chain 15 residue 97 THR Chi-restraints excluded: chain 15 residue 121 VAL Chi-restraints excluded: chain 15 residue 138 HIS Chi-restraints excluded: chain 15 residue 238 LEU Chi-restraints excluded: chain 15 residue 245 CYS Chi-restraints excluded: chain 15 residue 248 THR Chi-restraints excluded: chain 15 residue 253 VAL Chi-restraints excluded: chain 15 residue 271 PHE Chi-restraints excluded: chain 16 residue 148 GLU Chi-restraints excluded: chain 16 residue 209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 81 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 177 optimal weight: 0.0670 chunk 155 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 12 200 ASN 14 209 ASN ** 15 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 232 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.107610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.078998 restraints weight = 48995.108| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.47 r_work: 0.3034 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 2.243 25454 Z= 1.231 Angle : 1.063 43.966 36557 Z= 0.411 Chirality : 0.048 0.835 2923 Planarity : 0.005 0.049 4475 Dihedral : 25.276 174.890 7297 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.72 % Favored : 92.12 % Rotamer: Outliers : 2.32 % Allowed : 16.66 % Favored : 81.02 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.64 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1827 helix: 0.89 (0.16), residues: 998 sheet: None (None), residues: 0 loop : -1.46 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG15 225 TYR 0.016 0.001 TYR14 185 PHE 0.038 0.001 PHE15 271 TRP 0.013 0.001 TRP 6 130 HIS 0.006 0.002 HIS 7 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (25316) covalent geometry : angle 1.06253 / 0.41 (36557) hydrogen bonds : bond 0.04627 / 3.00 ( 718) hydrogen bonds : angle 4.15665 / 2.89 ( 2097) Misc. bond : bond 0.29738 / 17.14 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11370.58 seconds wall clock time: 193 minutes 57.11 seconds (11637.11 seconds total)