Starting phenix.real_space_refine on Sun Oct 13 11:55:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssp_25412/10_2024/7ssp_25412.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssp_25412/10_2024/7ssp_25412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssp_25412/10_2024/7ssp_25412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssp_25412/10_2024/7ssp_25412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssp_25412/10_2024/7ssp_25412.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssp_25412/10_2024/7ssp_25412.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5175 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 6909 2.51 5 N 1912 2.21 5 O 2040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 10930 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1433 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1436 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1433 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1433 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1298 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1299 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1299 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1299 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 6.85, per 1000 atoms: 0.63 Number of scatterers: 10930 At special positions: 0 Unit cell: (98.04, 108.3, 96.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 2040 8.00 N 1912 7.00 C 6909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 73.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.594A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 117 through 125 removed outlier: 4.037A pdb=" N ILE A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 166 Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 199 through 207 removed outlier: 3.878A pdb=" N ALA A 203 " --> pdb=" O HIS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 230 removed outlier: 4.148A pdb=" N TYR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 259 removed outlier: 3.684A pdb=" N THR A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 244 " --> pdb=" O TRP A 240 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 266 through 282 removed outlier: 4.668A pdb=" N ASP A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 108 removed outlier: 3.994A pdb=" N ARG B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 removed outlier: 4.381A pdb=" N ILE B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 144 through 169 removed outlier: 4.057A pdb=" N LEU B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 199 through 207 removed outlier: 3.871A pdb=" N ALA B 203 " --> pdb=" O HIS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 230 Processing helix chain 'B' and resid 238 through 259 removed outlier: 3.694A pdb=" N THR B 242 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG B 244 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 266 through 282 removed outlier: 4.908A pdb=" N ASP B 279 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 108 removed outlier: 3.893A pdb=" N ARG C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 125 through 127 No H-bonds generated for 'chain 'C' and resid 125 through 127' Processing helix chain 'C' and resid 142 through 166 removed outlier: 4.083A pdb=" N ILE C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 191 Processing helix chain 'C' and resid 199 through 207 removed outlier: 3.879A pdb=" N ALA C 203 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 229 Processing helix chain 'C' and resid 238 through 259 removed outlier: 3.636A pdb=" N THR C 242 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 243 " --> pdb=" O ASN C 239 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG C 244 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 266 through 282 removed outlier: 4.824A pdb=" N ASP C 279 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 280 " --> pdb=" O ARG C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 109 removed outlier: 3.832A pdb=" N ARG D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 4.264A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 166 removed outlier: 4.326A pdb=" N ILE D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 191 Processing helix chain 'D' and resid 199 through 207 removed outlier: 3.854A pdb=" N ALA D 203 " --> pdb=" O HIS D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 230 removed outlier: 4.131A pdb=" N TYR D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 259 removed outlier: 3.678A pdb=" N THR D 242 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG D 243 " --> pdb=" O ASN D 239 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG D 244 " --> pdb=" O TRP D 240 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE D 250 " --> pdb=" O MET D 246 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR D 254 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 266 through 282 removed outlier: 4.832A pdb=" N ASP D 279 " --> pdb=" O ASN D 275 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 280 " --> pdb=" O ARG D 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 74 removed outlier: 3.728A pdb=" N ILE E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE E 53 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 105 removed outlier: 3.930A pdb=" N ILE E 83 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE E 104 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 130 through 155 removed outlier: 3.971A pdb=" N ALA E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR E 138 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR E 155 " --> pdb=" O ASN E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 180 Processing helix chain 'E' and resid 197 through 205 Processing helix chain 'E' and resid 208 through 217 removed outlier: 3.643A pdb=" N SER E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU E 215 " --> pdb=" O ILE E 211 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 74 removed outlier: 4.456A pdb=" N ARG F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE F 52 " --> pdb=" O ALA F 48 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE F 53 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 104 removed outlier: 3.633A pdb=" N ILE F 83 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS F 85 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET F 86 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.520A pdb=" N ALA F 124 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 155 removed outlier: 3.825A pdb=" N VAL F 139 " --> pdb=" O MET F 135 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR F 155 " --> pdb=" O ASN F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 180 Processing helix chain 'F' and resid 195 through 217 removed outlier: 3.564A pdb=" N LEU F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY F 206 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE F 211 " --> pdb=" O CYS F 207 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR F 212 " --> pdb=" O ARG F 208 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG F 216 " --> pdb=" O TYR F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 74 removed outlier: 3.688A pdb=" N ILE G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 104 removed outlier: 3.718A pdb=" N ILE G 83 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE G 104 " --> pdb=" O LEU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 124 Processing helix chain 'G' and resid 136 through 155 removed outlier: 3.626A pdb=" N THR G 155 " --> pdb=" O ASN G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 180 Processing helix chain 'G' and resid 195 through 217 removed outlier: 3.586A pdb=" N LEU G 199 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY G 206 " --> pdb=" O ILE G 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE G 211 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 74 removed outlier: 3.818A pdb=" N ILE H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 104 removed outlier: 3.756A pdb=" N ILE H 83 " --> pdb=" O VAL H 79 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE H 104 " --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 124 Processing helix chain 'H' and resid 137 through 155 removed outlier: 3.614A pdb=" N THR H 155 " --> pdb=" O ASN H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 180 Processing helix chain 'H' and resid 195 through 217 removed outlier: 3.801A pdb=" N LEU H 199 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS H 200 " --> pdb=" O TYR H 196 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER H 201 " --> pdb=" O ALA H 197 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY H 206 " --> pdb=" O ILE H 202 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE H 211 " --> pdb=" O CYS H 207 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU H 215 " --> pdb=" O ILE H 211 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG H 216 " --> pdb=" O TYR H 212 " (cutoff:3.500A) 667 hydrogen bonds defined for protein. 1980 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: 2.88 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3676 1.34 - 1.46: 2044 1.46 - 1.58: 5292 1.58 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 11138 Sorted by residual: bond pdb=" CB VAL G 55 " pdb=" CG2 VAL G 55 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.77e+00 bond pdb=" C ILE C 194 " pdb=" N PRO C 195 " ideal model delta sigma weight residual 1.335 1.351 -0.015 1.30e-02 5.92e+03 1.39e+00 bond pdb=" CA LYS G 131 " pdb=" C LYS G 131 " ideal model delta sigma weight residual 1.523 1.504 0.020 1.80e-02 3.09e+03 1.18e+00 bond pdb=" CB VAL H 55 " pdb=" CG2 VAL H 55 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.73e-01 bond pdb=" N GLN B 172 " pdb=" CA GLN B 172 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.15e-02 7.56e+03 8.40e-01 ... (remaining 11133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 14679 1.66 - 3.32: 333 3.32 - 4.98: 47 4.98 - 6.64: 17 6.64 - 8.30: 2 Bond angle restraints: 15078 Sorted by residual: angle pdb=" N ALA E 124 " pdb=" CA ALA E 124 " pdb=" C ALA E 124 " ideal model delta sigma weight residual 114.56 108.60 5.96 1.27e+00 6.20e-01 2.20e+01 angle pdb=" N ALA G 124 " pdb=" CA ALA G 124 " pdb=" C ALA G 124 " ideal model delta sigma weight residual 114.56 108.66 5.90 1.27e+00 6.20e-01 2.16e+01 angle pdb=" N ALA F 124 " pdb=" CA ALA F 124 " pdb=" C ALA F 124 " ideal model delta sigma weight residual 114.56 108.73 5.83 1.27e+00 6.20e-01 2.11e+01 angle pdb=" N ALA H 124 " pdb=" CA ALA H 124 " pdb=" C ALA H 124 " ideal model delta sigma weight residual 114.56 108.75 5.81 1.27e+00 6.20e-01 2.09e+01 angle pdb=" N VAL H 117 " pdb=" CA VAL H 117 " pdb=" C VAL H 117 " ideal model delta sigma weight residual 113.42 108.52 4.90 1.17e+00 7.31e-01 1.76e+01 ... (remaining 15073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5958 17.79 - 35.58: 622 35.58 - 53.38: 116 53.38 - 71.17: 11 71.17 - 88.96: 11 Dihedral angle restraints: 6718 sinusoidal: 2702 harmonic: 4016 Sorted by residual: dihedral pdb=" CA GLU G 165 " pdb=" C GLU G 165 " pdb=" N GLU G 166 " pdb=" CA GLU G 166 " ideal model delta harmonic sigma weight residual 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA GLU H 165 " pdb=" C GLU H 165 " pdb=" N GLU H 166 " pdb=" CA GLU H 166 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA GLU F 165 " pdb=" C GLU F 165 " pdb=" N GLU F 166 " pdb=" CA GLU F 166 " ideal model delta harmonic sigma weight residual 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 6715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1011 0.029 - 0.058: 494 0.058 - 0.087: 145 0.087 - 0.117: 40 0.117 - 0.146: 6 Chirality restraints: 1696 Sorted by residual: chirality pdb=" CA MET C 281 " pdb=" N MET C 281 " pdb=" C MET C 281 " pdb=" CB MET C 281 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA PRO E 81 " pdb=" N PRO E 81 " pdb=" C PRO E 81 " pdb=" CB PRO E 81 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO G 81 " pdb=" N PRO G 81 " pdb=" C PRO G 81 " pdb=" CB PRO G 81 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 1693 not shown) Planarity restraints: 1940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 144 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.73e+00 pdb=" C GLU A 144 " -0.038 2.00e-02 2.50e+03 pdb=" O GLU A 144 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 145 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 112 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 111 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 112 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " -0.026 5.00e-02 4.00e+02 ... (remaining 1937 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2038 2.77 - 3.30: 10425 3.30 - 3.83: 16849 3.83 - 4.37: 18638 4.37 - 4.90: 32859 Nonbonded interactions: 80809 Sorted by model distance: nonbonded pdb=" OD2 ASP D 233 " pdb=" NH1 ARG D 244 " model vdw 2.232 3.120 nonbonded pdb=" OD2 ASP B 233 " pdb=" NH1 ARG B 244 " model vdw 2.236 3.120 nonbonded pdb=" OD2 ASP A 233 " pdb=" NH1 ARG A 244 " model vdw 2.310 3.120 nonbonded pdb=" O SER B 143 " pdb=" OG SER B 143 " model vdw 2.311 3.040 nonbonded pdb=" OD1 ASP D 233 " pdb=" NH1 ARG D 243 " model vdw 2.333 3.120 ... (remaining 80804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 93 through 127 or (resid 141 and (name N or name CA or nam \ e C or name O or name CB )) or resid 142 through 284)) selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 45 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB )) or resid 102 through 217)) selection = (chain 'F' and (resid 45 through 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB )) or resid 163 through 217)) selection = (chain 'G' and (resid 45 through 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB )) or resid 163 through 217)) selection = (chain 'H' and (resid 45 through 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB )) or resid 163 through 217)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.270 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11138 Z= 0.232 Angle : 0.626 8.298 15078 Z= 0.370 Chirality : 0.037 0.146 1696 Planarity : 0.005 0.053 1940 Dihedral : 14.584 88.962 4102 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.20), residues: 1344 helix: -1.28 (0.15), residues: 1000 sheet: None (None), residues: 0 loop : -4.52 (0.25), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 115 HIS 0.006 0.001 HIS E 147 PHE 0.010 0.001 PHE C 110 TYR 0.011 0.001 TYR G 212 ARG 0.004 0.000 ARG F 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.095 Fit side-chains REVERT: A 226 ASP cc_start: 0.7551 (m-30) cc_final: 0.7260 (m-30) REVERT: A 266 PHE cc_start: 0.7627 (m-80) cc_final: 0.7421 (m-80) REVERT: B 163 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6987 (tt0) REVERT: B 202 ARG cc_start: 0.7747 (tmt-80) cc_final: 0.7399 (tpt90) REVERT: C 159 ARG cc_start: 0.7449 (ttp-110) cc_final: 0.7075 (ttm-80) REVERT: C 167 LEU cc_start: 0.8274 (tp) cc_final: 0.8051 (tt) REVERT: C 202 ARG cc_start: 0.7749 (tmt-80) cc_final: 0.7450 (tpt90) REVERT: C 226 ASP cc_start: 0.7462 (m-30) cc_final: 0.7138 (m-30) REVERT: C 281 MET cc_start: 0.6922 (tpp) cc_final: 0.6527 (mmp) REVERT: D 119 GLU cc_start: 0.6020 (tm-30) cc_final: 0.5621 (tm-30) REVERT: D 226 ASP cc_start: 0.7512 (m-30) cc_final: 0.7253 (m-30) REVERT: D 266 PHE cc_start: 0.7658 (m-80) cc_final: 0.7437 (m-80) REVERT: D 281 MET cc_start: 0.6674 (mmm) cc_final: 0.6317 (mmp) REVERT: E 67 TYR cc_start: 0.8693 (m-10) cc_final: 0.7824 (m-10) REVERT: E 101 MET cc_start: 0.8400 (ttm) cc_final: 0.8057 (ttp) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.3367 time to fit residues: 118.5680 Evaluate side-chains 209 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN E 70 GLN E 147 HIS F 70 GLN F 147 HIS G 70 GLN G 147 HIS H 70 GLN H 147 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11138 Z= 0.273 Angle : 0.637 8.431 15078 Z= 0.325 Chirality : 0.039 0.136 1696 Planarity : 0.006 0.067 1940 Dihedral : 4.243 20.819 1488 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.22 % Allowed : 12.18 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.23), residues: 1344 helix: 0.35 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -3.93 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 115 HIS 0.006 0.001 HIS H 147 PHE 0.012 0.002 PHE B 266 TYR 0.015 0.002 TYR B 230 ARG 0.004 0.001 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 203 time to evaluate : 1.367 Fit side-chains REVERT: A 164 GLU cc_start: 0.7715 (tm-30) cc_final: 0.6911 (tt0) REVERT: A 226 ASP cc_start: 0.7550 (m-30) cc_final: 0.7250 (m-30) REVERT: B 164 GLU cc_start: 0.7742 (tm-30) cc_final: 0.6965 (tt0) REVERT: B 202 ARG cc_start: 0.7616 (tmt-80) cc_final: 0.7389 (tpt90) REVERT: B 208 MET cc_start: 0.8099 (ttm) cc_final: 0.7797 (mtt) REVERT: B 226 ASP cc_start: 0.7794 (m-30) cc_final: 0.7548 (m-30) REVERT: C 202 ARG cc_start: 0.7554 (tmt-80) cc_final: 0.7335 (tpt90) REVERT: C 226 ASP cc_start: 0.7488 (m-30) cc_final: 0.7200 (m-30) REVERT: D 226 ASP cc_start: 0.7537 (m-30) cc_final: 0.7237 (m-30) REVERT: D 281 MET cc_start: 0.6824 (mmm) cc_final: 0.6560 (mmp) REVERT: G 208 ARG cc_start: 0.7209 (tmt170) cc_final: 0.5854 (ttp80) REVERT: H 208 ARG cc_start: 0.7352 (tmt170) cc_final: 0.6179 (ttp80) outliers start: 14 outliers final: 13 residues processed: 213 average time/residue: 0.3231 time to fit residues: 91.6719 Evaluate side-chains 206 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 193 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 110 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 106 optimal weight: 0.1980 chunk 119 optimal weight: 0.0000 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 169 GLN B 234 GLN B 275 ASN C 275 ASN D 275 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11138 Z= 0.144 Angle : 0.530 7.459 15078 Z= 0.269 Chirality : 0.035 0.206 1696 Planarity : 0.005 0.064 1940 Dihedral : 3.784 19.759 1488 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.04 % Allowed : 14.36 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1344 helix: 1.31 (0.17), residues: 1028 sheet: None (None), residues: 0 loop : -3.51 (0.30), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 115 HIS 0.003 0.001 HIS A 211 PHE 0.007 0.001 PHE B 266 TYR 0.006 0.001 TYR G 212 ARG 0.005 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 210 time to evaluate : 1.155 Fit side-chains REVERT: A 114 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.7103 (t-90) REVERT: A 164 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6882 (tt0) REVERT: A 208 MET cc_start: 0.7895 (ttm) cc_final: 0.7590 (mtt) REVERT: B 164 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7014 (tt0) REVERT: B 208 MET cc_start: 0.7929 (ttm) cc_final: 0.7621 (mtt) REVERT: C 202 ARG cc_start: 0.7528 (tmt-80) cc_final: 0.7298 (tpt90) REVERT: C 208 MET cc_start: 0.7963 (ttm) cc_final: 0.7655 (mtt) REVERT: D 123 GLU cc_start: 0.7029 (tt0) cc_final: 0.6576 (tm-30) REVERT: D 208 MET cc_start: 0.7916 (ttm) cc_final: 0.7600 (mtt) REVERT: D 281 MET cc_start: 0.6804 (mmm) cc_final: 0.6488 (mmp) REVERT: E 67 TYR cc_start: 0.8614 (m-10) cc_final: 0.7926 (m-10) REVERT: E 135 MET cc_start: 0.7756 (mmp) cc_final: 0.7388 (mmt) REVERT: F 67 TYR cc_start: 0.8594 (m-10) cc_final: 0.7988 (m-10) REVERT: F 208 ARG cc_start: 0.7166 (tmt170) cc_final: 0.6107 (ttp80) REVERT: G 67 TYR cc_start: 0.8658 (m-10) cc_final: 0.8028 (m-10) REVERT: H 67 TYR cc_start: 0.8666 (m-10) cc_final: 0.7999 (m-10) REVERT: H 208 ARG cc_start: 0.7201 (tmt170) cc_final: 0.6082 (ttp80) outliers start: 12 outliers final: 7 residues processed: 219 average time/residue: 0.2806 time to fit residues: 82.2466 Evaluate side-chains 187 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 127 optimal weight: 0.1980 chunk 114 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 169 GLN B 275 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11138 Z= 0.144 Angle : 0.520 7.639 15078 Z= 0.262 Chirality : 0.035 0.196 1696 Planarity : 0.005 0.057 1940 Dihedral : 3.607 19.232 1488 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.48 % Allowed : 15.49 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1344 helix: 1.65 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -3.29 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 115 HIS 0.004 0.001 HIS D 229 PHE 0.008 0.001 PHE B 266 TYR 0.015 0.001 TYR H 212 ARG 0.006 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: A 114 HIS cc_start: 0.7776 (OUTLIER) cc_final: 0.7158 (t-90) REVERT: A 164 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6872 (tt0) REVERT: A 208 MET cc_start: 0.7869 (ttm) cc_final: 0.7622 (mtt) REVERT: B 164 GLU cc_start: 0.7686 (tm-30) cc_final: 0.6947 (tt0) REVERT: B 208 MET cc_start: 0.7907 (ttm) cc_final: 0.7656 (mtt) REVERT: C 196 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: C 202 ARG cc_start: 0.7518 (tmt-80) cc_final: 0.7306 (tpt90) REVERT: C 208 MET cc_start: 0.7978 (ttm) cc_final: 0.7692 (mtt) REVERT: D 123 GLU cc_start: 0.7085 (tt0) cc_final: 0.6630 (tm-30) REVERT: D 208 MET cc_start: 0.7940 (ttm) cc_final: 0.7714 (mtt) REVERT: D 281 MET cc_start: 0.6911 (mmm) cc_final: 0.6661 (mmp) REVERT: E 67 TYR cc_start: 0.8651 (m-10) cc_final: 0.8002 (m-10) REVERT: E 135 MET cc_start: 0.7749 (mmp) cc_final: 0.7433 (mmt) REVERT: F 67 TYR cc_start: 0.8596 (m-10) cc_final: 0.7982 (m-10) REVERT: F 208 ARG cc_start: 0.7053 (tmt170) cc_final: 0.5896 (ttp80) REVERT: G 67 TYR cc_start: 0.8656 (m-10) cc_final: 0.8061 (m-10) REVERT: G 208 ARG cc_start: 0.7029 (tmt170) cc_final: 0.6052 (ttp80) REVERT: H 67 TYR cc_start: 0.8654 (m-10) cc_final: 0.8012 (m-10) REVERT: H 208 ARG cc_start: 0.7204 (tmt170) cc_final: 0.6056 (ttp80) outliers start: 17 outliers final: 12 residues processed: 196 average time/residue: 0.3354 time to fit residues: 87.5183 Evaluate side-chains 188 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 174 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 108 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 32 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 169 GLN C 275 ASN D 275 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11138 Z= 0.146 Angle : 0.515 7.266 15078 Z= 0.259 Chirality : 0.035 0.198 1696 Planarity : 0.004 0.052 1940 Dihedral : 3.513 18.789 1488 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.57 % Allowed : 15.93 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1344 helix: 1.91 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -3.09 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 115 HIS 0.004 0.001 HIS D 229 PHE 0.011 0.001 PHE B 266 TYR 0.007 0.001 TYR B 230 ARG 0.005 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 114 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7171 (t-90) REVERT: A 164 GLU cc_start: 0.7577 (tm-30) cc_final: 0.6816 (tt0) REVERT: B 159 ARG cc_start: 0.7368 (ttm-80) cc_final: 0.6902 (ttm-80) REVERT: B 164 GLU cc_start: 0.7623 (tm-30) cc_final: 0.6919 (tt0) REVERT: B 208 MET cc_start: 0.7829 (ttm) cc_final: 0.7582 (mtt) REVERT: C 164 GLU cc_start: 0.7488 (tp30) cc_final: 0.6589 (tt0) REVERT: C 196 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: C 208 MET cc_start: 0.7937 (ttm) cc_final: 0.7671 (mtt) REVERT: D 159 ARG cc_start: 0.7355 (ttm-80) cc_final: 0.6857 (ttm-80) REVERT: D 175 LYS cc_start: 0.8061 (tttm) cc_final: 0.7753 (ttpp) REVERT: D 208 MET cc_start: 0.7892 (ttm) cc_final: 0.7672 (mtt) REVERT: D 281 MET cc_start: 0.6887 (mmm) cc_final: 0.6618 (mmp) REVERT: E 67 TYR cc_start: 0.8674 (m-10) cc_final: 0.8022 (m-10) REVERT: E 135 MET cc_start: 0.7774 (mmp) cc_final: 0.7486 (mmt) REVERT: F 67 TYR cc_start: 0.8593 (m-10) cc_final: 0.8060 (m-10) REVERT: F 208 ARG cc_start: 0.7113 (tmt170) cc_final: 0.5747 (ttp80) REVERT: G 67 TYR cc_start: 0.8665 (m-10) cc_final: 0.8062 (m-10) REVERT: G 208 ARG cc_start: 0.6988 (tmt170) cc_final: 0.6057 (ttp80) REVERT: H 67 TYR cc_start: 0.8666 (m-10) cc_final: 0.8034 (m-10) REVERT: H 208 ARG cc_start: 0.7203 (tmt170) cc_final: 0.6056 (ttp80) outliers start: 18 outliers final: 11 residues processed: 188 average time/residue: 0.3022 time to fit residues: 76.4125 Evaluate side-chains 183 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 106 optimal weight: 0.0870 chunk 59 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 275 ASN G 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11138 Z= 0.144 Angle : 0.513 7.351 15078 Z= 0.256 Chirality : 0.035 0.204 1696 Planarity : 0.004 0.050 1940 Dihedral : 3.431 19.084 1488 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.31 % Allowed : 16.45 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1344 helix: 2.18 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -2.92 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 115 HIS 0.003 0.001 HIS D 229 PHE 0.009 0.001 PHE B 266 TYR 0.014 0.001 TYR G 212 ARG 0.006 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 176 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: A 114 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7117 (t-90) REVERT: A 164 GLU cc_start: 0.7517 (tm-30) cc_final: 0.6885 (tt0) REVERT: B 164 GLU cc_start: 0.7555 (tm-30) cc_final: 0.6899 (tt0) REVERT: B 208 MET cc_start: 0.7832 (ttm) cc_final: 0.7609 (mtt) REVERT: B 227 MET cc_start: 0.7800 (ttp) cc_final: 0.7547 (ttp) REVERT: C 159 ARG cc_start: 0.7326 (ttm-80) cc_final: 0.6838 (ttm-80) REVERT: C 164 GLU cc_start: 0.7486 (tp30) cc_final: 0.6603 (tt0) REVERT: C 208 MET cc_start: 0.7934 (ttm) cc_final: 0.7681 (mtt) REVERT: D 175 LYS cc_start: 0.8082 (tttm) cc_final: 0.7788 (ttpp) REVERT: D 281 MET cc_start: 0.6998 (mmm) cc_final: 0.6758 (mmp) REVERT: E 67 TYR cc_start: 0.8670 (m-10) cc_final: 0.8172 (m-10) REVERT: E 135 MET cc_start: 0.7787 (mmp) cc_final: 0.7529 (mmt) REVERT: F 67 TYR cc_start: 0.8587 (m-10) cc_final: 0.8062 (m-10) REVERT: F 208 ARG cc_start: 0.7003 (tmt170) cc_final: 0.5813 (ttp80) REVERT: G 67 TYR cc_start: 0.8708 (m-10) cc_final: 0.8207 (m-10) REVERT: G 208 ARG cc_start: 0.6948 (tmt170) cc_final: 0.6021 (ttp80) REVERT: H 67 TYR cc_start: 0.8671 (m-10) cc_final: 0.8050 (m-10) REVERT: H 208 ARG cc_start: 0.7205 (tmt170) cc_final: 0.5962 (ttp80) outliers start: 15 outliers final: 9 residues processed: 187 average time/residue: 0.2783 time to fit residues: 71.1394 Evaluate side-chains 180 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 ASN C 275 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11138 Z= 0.181 Angle : 0.542 7.995 15078 Z= 0.270 Chirality : 0.036 0.211 1696 Planarity : 0.004 0.049 1940 Dihedral : 3.521 18.948 1488 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.65 % Allowed : 16.80 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.25), residues: 1344 helix: 2.23 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -2.74 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 200 HIS 0.003 0.001 HIS D 229 PHE 0.011 0.001 PHE C 110 TYR 0.018 0.001 TYR H 212 ARG 0.005 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7561 (tm-30) cc_final: 0.6835 (tt0) REVERT: B 164 GLU cc_start: 0.7608 (tm-30) cc_final: 0.6946 (tt0) REVERT: B 227 MET cc_start: 0.7853 (ttp) cc_final: 0.7573 (ttp) REVERT: B 261 ASP cc_start: 0.8510 (t70) cc_final: 0.8172 (t70) REVERT: C 196 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.7250 (m-80) REVERT: D 110 PHE cc_start: 0.5945 (p90) cc_final: 0.5709 (p90) REVERT: D 175 LYS cc_start: 0.8079 (tttm) cc_final: 0.7778 (ttpp) REVERT: D 281 MET cc_start: 0.7000 (mmm) cc_final: 0.6751 (mmp) REVERT: E 67 TYR cc_start: 0.8650 (m-10) cc_final: 0.8082 (m-10) REVERT: E 135 MET cc_start: 0.7800 (mmp) cc_final: 0.7518 (mmt) REVERT: F 208 ARG cc_start: 0.7010 (tmt170) cc_final: 0.5812 (ttp80) REVERT: G 208 ARG cc_start: 0.6944 (tmt170) cc_final: 0.5945 (ttp80) REVERT: H 208 ARG cc_start: 0.7227 (tmt170) cc_final: 0.5988 (ttp80) outliers start: 19 outliers final: 14 residues processed: 183 average time/residue: 0.3011 time to fit residues: 75.0234 Evaluate side-chains 181 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 ASN C 275 ASN D 275 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11138 Z= 0.169 Angle : 0.531 8.246 15078 Z= 0.265 Chirality : 0.036 0.206 1696 Planarity : 0.004 0.049 1940 Dihedral : 3.496 18.749 1488 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.74 % Allowed : 16.97 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.25), residues: 1344 helix: 2.36 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -2.64 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 200 HIS 0.003 0.001 HIS D 229 PHE 0.010 0.001 PHE C 110 TYR 0.008 0.001 TYR B 230 ARG 0.006 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7543 (tm-30) cc_final: 0.6867 (tt0) REVERT: B 164 GLU cc_start: 0.7465 (tm-30) cc_final: 0.6957 (tt0) REVERT: B 227 MET cc_start: 0.7851 (ttp) cc_final: 0.7581 (ttp) REVERT: C 196 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: D 110 PHE cc_start: 0.5624 (p90) cc_final: 0.5384 (p90) REVERT: D 175 LYS cc_start: 0.8071 (tttm) cc_final: 0.7793 (ttpp) REVERT: D 281 MET cc_start: 0.6981 (mmm) cc_final: 0.6745 (mmp) REVERT: E 67 TYR cc_start: 0.8686 (m-10) cc_final: 0.8131 (m-10) REVERT: E 135 MET cc_start: 0.7777 (mmp) cc_final: 0.7499 (mmt) REVERT: F 208 ARG cc_start: 0.7038 (tmt170) cc_final: 0.5775 (ttp80) REVERT: G 208 ARG cc_start: 0.7014 (tmt170) cc_final: 0.5971 (ttp80) REVERT: H 208 ARG cc_start: 0.7238 (tmt170) cc_final: 0.5980 (ttp80) outliers start: 20 outliers final: 14 residues processed: 182 average time/residue: 0.3023 time to fit residues: 75.2195 Evaluate side-chains 177 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 107 optimal weight: 0.0970 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 76 optimal weight: 0.0370 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 ASN C 275 ASN D 275 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11138 Z= 0.135 Angle : 0.513 8.198 15078 Z= 0.256 Chirality : 0.035 0.210 1696 Planarity : 0.004 0.049 1940 Dihedral : 3.400 18.506 1488 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.57 % Allowed : 17.32 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.25), residues: 1344 helix: 2.56 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -2.54 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 115 HIS 0.003 0.001 HIS D 229 PHE 0.014 0.001 PHE C 110 TYR 0.006 0.001 TYR B 230 ARG 0.006 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7503 (tm-30) cc_final: 0.6882 (tt0) REVERT: B 164 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6842 (tt0) REVERT: B 227 MET cc_start: 0.7865 (ttp) cc_final: 0.7630 (ttp) REVERT: C 164 GLU cc_start: 0.7398 (tp30) cc_final: 0.6545 (tt0) REVERT: C 196 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: C 216 SER cc_start: 0.8478 (t) cc_final: 0.8166 (m) REVERT: D 114 HIS cc_start: 0.7346 (m-70) cc_final: 0.6697 (t-90) REVERT: D 159 ARG cc_start: 0.7351 (ttm-80) cc_final: 0.6818 (ttm-80) REVERT: D 175 LYS cc_start: 0.8069 (tttm) cc_final: 0.7814 (ttpp) REVERT: D 281 MET cc_start: 0.6966 (mmm) cc_final: 0.6739 (mmp) REVERT: E 67 TYR cc_start: 0.8656 (m-10) cc_final: 0.8141 (m-10) REVERT: E 135 MET cc_start: 0.7727 (mmp) cc_final: 0.7450 (mmt) REVERT: F 208 ARG cc_start: 0.7095 (tmt170) cc_final: 0.5651 (ttp80) REVERT: G 208 ARG cc_start: 0.7067 (tmt170) cc_final: 0.6047 (ttp80) REVERT: H 67 TYR cc_start: 0.8729 (m-10) cc_final: 0.8203 (m-10) REVERT: H 208 ARG cc_start: 0.7132 (tmt170) cc_final: 0.5936 (ttp80) outliers start: 18 outliers final: 12 residues processed: 181 average time/residue: 0.2822 time to fit residues: 69.9967 Evaluate side-chains 177 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 164 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 ASN C 275 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11138 Z= 0.142 Angle : 0.513 8.215 15078 Z= 0.256 Chirality : 0.035 0.213 1696 Planarity : 0.004 0.051 1940 Dihedral : 3.344 18.339 1488 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.13 % Allowed : 17.75 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.25), residues: 1344 helix: 2.69 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -2.24 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 115 HIS 0.003 0.001 HIS D 229 PHE 0.015 0.001 PHE C 110 TYR 0.013 0.001 TYR G 212 ARG 0.006 0.000 ARG B 159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7487 (tm-30) cc_final: 0.6873 (tt0) REVERT: B 159 ARG cc_start: 0.7405 (ttm-80) cc_final: 0.6870 (ttm-80) REVERT: B 164 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6840 (tt0) REVERT: B 227 MET cc_start: 0.7871 (ttp) cc_final: 0.7614 (ttp) REVERT: C 159 ARG cc_start: 0.7362 (ttm-80) cc_final: 0.6832 (ttm-80) REVERT: C 164 GLU cc_start: 0.7343 (tp30) cc_final: 0.6542 (tt0) REVERT: C 196 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: C 216 SER cc_start: 0.8474 (t) cc_final: 0.8170 (m) REVERT: D 114 HIS cc_start: 0.7425 (m-70) cc_final: 0.6732 (t-90) REVERT: D 164 GLU cc_start: 0.7518 (tp30) cc_final: 0.6740 (tt0) REVERT: D 175 LYS cc_start: 0.8047 (tttm) cc_final: 0.7823 (ttpp) REVERT: D 281 MET cc_start: 0.7009 (mmm) cc_final: 0.6759 (mmp) REVERT: E 67 TYR cc_start: 0.8600 (m-10) cc_final: 0.8197 (m-10) REVERT: E 135 MET cc_start: 0.7697 (mmp) cc_final: 0.7425 (mmt) REVERT: F 208 ARG cc_start: 0.7089 (tmt170) cc_final: 0.5640 (ttp80) REVERT: G 208 ARG cc_start: 0.7241 (tmt170) cc_final: 0.6182 (ttp80) REVERT: H 67 TYR cc_start: 0.8738 (m-10) cc_final: 0.8337 (m-10) REVERT: H 208 ARG cc_start: 0.7126 (tmt170) cc_final: 0.5935 (ttp80) outliers start: 13 outliers final: 12 residues processed: 182 average time/residue: 0.2841 time to fit residues: 71.7987 Evaluate side-chains 179 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 ASN D 275 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.153452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125457 restraints weight = 13314.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128313 restraints weight = 8782.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.130018 restraints weight = 6811.860| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4685 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: