Starting phenix.real_space_refine on Wed Jun 26 16:23:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6e_28881/06_2024/8f6e_28881.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6e_28881/06_2024/8f6e_28881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6e_28881/06_2024/8f6e_28881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6e_28881/06_2024/8f6e_28881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6e_28881/06_2024/8f6e_28881.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6e_28881/06_2024/8f6e_28881.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 28 5.16 5 C 6678 2.51 5 N 1760 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C ASP 169": "OD1" <-> "OD2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F ASP 76": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 10478 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2172 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain: "C" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1474 Classifications: {'peptide': 192} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "D" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "B" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2172 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1474 Classifications: {'peptide': 192} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "F" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.11, per 1000 atoms: 0.58 Number of scatterers: 10478 At special positions: 0 Unit cell: (67.284, 156.996, 144.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 28 16.00 O 2004 8.00 N 1760 7.00 C 6678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.48 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 250 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 234 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" ND1 HIS A 73 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 77 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 155 " pdb=" ZN A 304 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS B 263 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS A 285 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS A 263 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 285 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" ND1 HIS B 250 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 234 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" ND1 HIS B 73 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 77 " pdb=" ZN B 304 " pdb="ZN ZN B 304 " - pdb=" NE2 HIS B 155 " 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 23 sheets defined 31.8% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 11 through 32 removed outlier: 3.565A pdb=" N SER A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 28 " --> pdb=" O THR A 24 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 67 removed outlier: 4.067A pdb=" N LEU A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 109 removed outlier: 3.613A pdb=" N ALA A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 142 removed outlier: 3.723A pdb=" N VAL A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 175 removed outlier: 3.529A pdb=" N SER A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 208 removed outlier: 3.600A pdb=" N TYR A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 222 removed outlier: 3.758A pdb=" N ARG A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 222 " --> pdb=" O GLN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 277 removed outlier: 3.655A pdb=" N SER A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 130 removed outlier: 4.200A pdb=" N LYS C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 124 through 130' Processing helix chain 'C' and resid 184 through 190 removed outlier: 3.641A pdb=" N GLU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.983A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 34 removed outlier: 3.507A pdb=" N SER B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE B 28 " --> pdb=" O THR B 24 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 67 removed outlier: 3.954A pdb=" N ALA B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 109 removed outlier: 3.668A pdb=" N ALA B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 142 removed outlier: 3.561A pdb=" N GLY B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA B 132 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 175 removed outlier: 3.667A pdb=" N LEU B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 208 removed outlier: 4.061A pdb=" N ASP B 181 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU B 183 " --> pdb=" O TRP B 179 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 removed outlier: 3.798A pdb=" N ARG B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 221 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 277 removed outlier: 3.650A pdb=" N SER B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 130 removed outlier: 4.234A pdb=" N LYS E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY E 130 " --> pdb=" O GLN E 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 124 through 130' Processing helix chain 'E' and resid 184 through 190 removed outlier: 3.654A pdb=" N GLU E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.975A pdb=" N THR F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 234 removed outlier: 3.808A pdb=" N GLY A 232 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 252 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 234 " --> pdb=" O HIS A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 234 removed outlier: 3.808A pdb=" N GLY A 232 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 252 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 234 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 249 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.977A pdb=" N GLU C 107 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 20 through 25 removed outlier: 3.801A pdb=" N VAL C 20 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 76 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.879A pdb=" N THR C 99 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.508A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 48 through 54 removed outlier: 7.062A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 76 removed outlier: 3.879A pdb=" N THR D 81 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AB2, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.537A pdb=" N LYS D 160 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY D 156 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.537A pdb=" N LYS D 160 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY D 156 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER D 194 " --> pdb=" O VAL D 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 170 through 171 removed outlier: 3.810A pdb=" N ASN D 214 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS D 213 " --> pdb=" O LYS D 226 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS D 226 " --> pdb=" O CYS D 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 232 through 241 removed outlier: 6.152A pdb=" N LEU B 233 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASP B 235 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS B 250 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B 249 " --> pdb=" O ILE B 283 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.868A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE E 76 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.982A pdb=" N GLU E 107 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 90 through 91 removed outlier: 3.769A pdb=" N THR E 99 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.861A pdb=" N ASN E 140 " --> pdb=" O TYR E 175 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR E 175 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 6 through 10 removed outlier: 3.602A pdb=" N VAL F 8 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU F 23 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR F 81 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 48 through 53 removed outlier: 7.073A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 106 through 107 Processing sheet with id=AC4, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.540A pdb=" N LYS F 160 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 167 through 171 removed outlier: 3.823A pdb=" N ASN F 214 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS F 213 " --> pdb=" O LYS F 226 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS F 226 " --> pdb=" O CYS F 213 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1170 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: 2.67 Time building geometry restraints manager: 3.92 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: 3352 1.34 - 1.46: 2439 1.46 - 1.58: 4869 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 10698 Sorted by residual: bond pdb=" N THR B 147 " pdb=" CA THR B 147 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.65e+00 bond pdb=" N THR A 147 " pdb=" CA THR A 147 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.35e+00 bond pdb=" CG PRO E 96 " pdb=" CD PRO E 96 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.26e+00 bond pdb=" CB TRP D 50 " pdb=" CG TRP D 50 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.04e+00 bond pdb=" CB TRP C 95 " pdb=" CG TRP C 95 " ideal model delta sigma weight residual 1.498 1.467 0.031 3.10e-02 1.04e+03 9.70e-01 ... (remaining 10693 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.37: 178 105.37 - 112.56: 5755 112.56 - 119.74: 3319 119.74 - 126.92: 5168 126.92 - 134.10: 142 Bond angle restraints: 14562 Sorted by residual: angle pdb=" C GLN F 132 " pdb=" N ILE F 133 " pdb=" CA ILE F 133 " ideal model delta sigma weight residual 121.97 128.84 -6.87 1.80e+00 3.09e-01 1.46e+01 angle pdb=" C GLN D 132 " pdb=" N ILE D 133 " pdb=" CA ILE D 133 " ideal model delta sigma weight residual 121.97 127.64 -5.67 1.80e+00 3.09e-01 9.92e+00 angle pdb=" C PHE D 163 " pdb=" N PRO D 164 " pdb=" CD PRO D 164 " ideal model delta sigma weight residual 120.60 126.49 -5.89 2.20e+00 2.07e-01 7.16e+00 angle pdb=" C PHE D 163 " pdb=" N PRO D 164 " pdb=" CA PRO D 164 " ideal model delta sigma weight residual 127.00 120.72 6.28 2.40e+00 1.74e-01 6.85e+00 angle pdb=" C THR B 147 " pdb=" CA THR B 147 " pdb=" CB THR B 147 " ideal model delta sigma weight residual 110.42 115.52 -5.10 1.99e+00 2.53e-01 6.57e+00 ... (remaining 14557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 5752 17.84 - 35.67: 496 35.67 - 53.51: 78 53.51 - 71.35: 19 71.35 - 89.19: 7 Dihedral angle restraints: 6352 sinusoidal: 2378 harmonic: 3974 Sorted by residual: dihedral pdb=" CB CYS D 25 " pdb=" SG CYS D 25 " pdb=" SG CYS D 99 " pdb=" CB CYS D 99 " ideal model delta sinusoidal sigma weight residual 93.00 170.21 -77.21 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS F 25 " pdb=" SG CYS F 25 " pdb=" SG CYS F 99 " pdb=" CB CYS F 99 " ideal model delta sinusoidal sigma weight residual 93.00 149.33 -56.33 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 148.60 -55.60 1 1.00e+01 1.00e-02 4.18e+01 ... (remaining 6349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 986 0.027 - 0.055: 470 0.055 - 0.082: 134 0.082 - 0.109: 80 0.109 - 0.137: 24 Chirality restraints: 1694 Sorted by residual: chirality pdb=" CA ILE E 49 " pdb=" N ILE E 49 " pdb=" C ILE E 49 " pdb=" CB ILE E 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE C 49 " pdb=" N ILE C 49 " pdb=" C ILE C 49 " pdb=" CB ILE C 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA VAL D 96 " pdb=" N VAL D 96 " pdb=" C VAL D 96 " pdb=" CB VAL D 96 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1691 not shown) Planarity restraints: 1834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F 163 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO F 164 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO F 164 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 164 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 165 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO D 166 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 166 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 166 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 165 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO F 166 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO F 166 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 166 " -0.024 5.00e-02 4.00e+02 ... (remaining 1831 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 111 2.63 - 3.20: 9498 3.20 - 3.76: 15343 3.76 - 4.33: 20423 4.33 - 4.90: 34211 Nonbonded interactions: 79586 Sorted by model distance: nonbonded pdb=" OD2 ASP B 287 " pdb="ZN ZN B 302 " model vdw 2.060 2.230 nonbonded pdb=" OD1 ASP A 287 " pdb="ZN ZN A 304 " model vdw 2.062 2.230 nonbonded pdb=" OD1 ASP B 287 " pdb="ZN ZN B 301 " model vdw 2.066 2.230 nonbonded pdb=" OD2 ASP A 287 " pdb="ZN ZN A 301 " model vdw 2.071 2.230 nonbonded pdb=" OD1 ASP A 159 " pdb="ZN ZN A 303 " model vdw 2.090 2.230 ... (remaining 79581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 1.930 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: 7.600 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.110 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 0.003 0.032 10698 Z= 0.184 Angle : 0.546 6.869 14562 Z= 0.278 Chirality : 0.039 0.137 1694 Planarity : 0.004 0.075 1834 Dihedral : 13.515 89.186 3774 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.44 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.77 (0.24), residues: 1342 helix: 0.28 (0.27), residues: 364 sheet: -0.84 (0.30), residues: 342 loop : -0.67 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 179 HIS 0.002 0.001 HIS C 200 PHE 0.010 0.001 PHE D 183 TYR 0.012 0.001 TYR A 201 ARG 0.004 0.000 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 139 PHE cc_start: 0.6512 (m-80) cc_final: 0.6287 (m-10) REVERT: F 223 LYS cc_start: 0.8204 (mppt) cc_final: 0.7926 (mppt) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2120 time to fit residues: 70.0996 Evaluate side-chains 203 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 78 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 HIS ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 HIS E 91 GLN E 140 ASN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10698 Z= 0.301 Angle : 0.642 9.212 14562 Z= 0.326 Chirality : 0.042 0.162 1694 Planarity : 0.004 0.059 1834 Dihedral : 4.345 16.232 1466 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.86 % Favored : 92.70 % Rotamer: Outliers : 1.40 % Allowed : 10.30 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -0.94 (0.23), residues: 1342 helix: 0.32 (0.26), residues: 400 sheet: -1.06 (0.28), residues: 364 loop : -0.86 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 171 HIS 0.003 0.001 HIS E 200 PHE 0.027 0.002 PHE C 141 TYR 0.029 0.002 TYR E 142 ARG 0.004 0.000 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 234 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ILE cc_start: 0.9326 (mm) cc_final: 0.9035 (mt) REVERT: A 278 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6742 (mm-30) REVERT: E 91 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8092 (pp30) REVERT: F 86 MET cc_start: 0.8195 (mtp) cc_final: 0.7967 (mtp) REVERT: F 192 LEU cc_start: 0.6264 (mp) cc_final: 0.6022 (mp) REVERT: F 223 LYS cc_start: 0.8275 (mppt) cc_final: 0.8021 (mppt) outliers start: 16 outliers final: 13 residues processed: 243 average time/residue: 0.2166 time to fit residues: 73.8236 Evaluate side-chains 226 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 212 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 213 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 20.0000 chunk 37 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 0.4980 chunk 121 optimal weight: 0.7980 chunk 131 optimal weight: 0.0670 chunk 108 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 91 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10698 Z= 0.182 Angle : 0.599 11.752 14562 Z= 0.297 Chirality : 0.041 0.167 1694 Planarity : 0.004 0.054 1834 Dihedral : 4.106 14.788 1466 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.51 % Favored : 93.96 % Rotamer: Outliers : 1.31 % Allowed : 13.87 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1342 helix: 0.41 (0.26), residues: 400 sheet: -1.01 (0.28), residues: 350 loop : -0.88 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 179 HIS 0.002 0.001 HIS A 285 PHE 0.036 0.002 PHE B 184 TYR 0.027 0.001 TYR E 142 ARG 0.005 0.000 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 217 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 GLU cc_start: 0.7931 (tp30) cc_final: 0.7673 (tp30) REVERT: F 86 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7953 (mtp) REVERT: F 223 LYS cc_start: 0.8215 (mppt) cc_final: 0.7925 (mppt) outliers start: 15 outliers final: 10 residues processed: 225 average time/residue: 0.2196 time to fit residues: 69.8923 Evaluate side-chains 214 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 203 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 196 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 122 optimal weight: 0.0370 chunk 129 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 10698 Z= 0.344 Angle : 0.646 7.905 14562 Z= 0.328 Chirality : 0.043 0.157 1694 Planarity : 0.004 0.050 1834 Dihedral : 4.429 17.014 1466 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.63 % Favored : 92.85 % Rotamer: Outliers : 1.75 % Allowed : 18.50 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -1.08 (0.23), residues: 1342 helix: 0.41 (0.26), residues: 400 sheet: -1.26 (0.27), residues: 366 loop : -1.01 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 171 HIS 0.004 0.001 HIS A 234 PHE 0.027 0.002 PHE C 141 TYR 0.026 0.002 TYR E 142 ARG 0.004 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 223 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ILE cc_start: 0.9299 (mm) cc_final: 0.8892 (mt) REVERT: C 91 GLN cc_start: 0.8415 (pp30) cc_final: 0.7909 (pp30) REVERT: D 92 GLU cc_start: 0.8015 (tp30) cc_final: 0.7734 (tp30) REVERT: D 168 THR cc_start: 0.7123 (OUTLIER) cc_final: 0.6843 (p) REVERT: B 58 ASN cc_start: 0.7633 (t0) cc_final: 0.7182 (t0) REVERT: B 201 TYR cc_start: 0.6717 (t80) cc_final: 0.6443 (t80) REVERT: E 91 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8013 (pp30) REVERT: F 86 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7913 (mtp) REVERT: F 111 ARG cc_start: 0.7538 (mmp-170) cc_final: 0.7143 (mmp-170) outliers start: 20 outliers final: 14 residues processed: 235 average time/residue: 0.2207 time to fit residues: 73.0643 Evaluate side-chains 220 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 203 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 212 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 0.0980 chunk 110 optimal weight: 0.0030 chunk 89 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN E 91 GLN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10698 Z= 0.201 Angle : 0.624 11.870 14562 Z= 0.306 Chirality : 0.042 0.159 1694 Planarity : 0.004 0.051 1834 Dihedral : 4.223 15.558 1466 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.44 % Favored : 94.04 % Rotamer: Outliers : 2.01 % Allowed : 19.63 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: 1342 helix: 0.47 (0.26), residues: 400 sheet: -1.18 (0.27), residues: 352 loop : -0.99 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 179 HIS 0.002 0.000 HIS E 200 PHE 0.039 0.002 PHE B 184 TYR 0.029 0.001 TYR E 142 ARG 0.002 0.000 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 TYR cc_start: 0.7353 (t80) cc_final: 0.7130 (t80) REVERT: C 91 GLN cc_start: 0.8406 (pp30) cc_final: 0.7925 (pp30) REVERT: D 92 GLU cc_start: 0.7942 (tp30) cc_final: 0.7686 (tp30) REVERT: D 168 THR cc_start: 0.7078 (OUTLIER) cc_final: 0.6730 (p) REVERT: B 58 ASN cc_start: 0.7593 (t0) cc_final: 0.7145 (t0) REVERT: B 201 TYR cc_start: 0.6770 (t80) cc_final: 0.6489 (t80) REVERT: E 91 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7916 (pp30) REVERT: E 107 GLU cc_start: 0.8377 (pm20) cc_final: 0.8074 (pm20) REVERT: F 86 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7968 (mtp) outliers start: 23 outliers final: 14 residues processed: 225 average time/residue: 0.1979 time to fit residues: 63.5694 Evaluate side-chains 213 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 95 TRP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 212 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 0.0020 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10698 Z= 0.296 Angle : 0.651 13.379 14562 Z= 0.324 Chirality : 0.043 0.159 1694 Planarity : 0.004 0.049 1834 Dihedral : 4.343 16.650 1466 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.08 % Favored : 92.40 % Rotamer: Outliers : 2.97 % Allowed : 20.24 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -1.13 (0.23), residues: 1342 helix: 0.44 (0.26), residues: 400 sheet: -1.29 (0.27), residues: 360 loop : -1.10 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 179 HIS 0.003 0.001 HIS D 112 PHE 0.028 0.002 PHE C 141 TYR 0.029 0.002 TYR E 142 ARG 0.004 0.000 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 209 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLN cc_start: 0.8397 (pp30) cc_final: 0.7865 (pp30) REVERT: D 92 GLU cc_start: 0.7955 (tp30) cc_final: 0.7690 (tp30) REVERT: D 168 THR cc_start: 0.7055 (OUTLIER) cc_final: 0.6690 (p) REVERT: B 58 ASN cc_start: 0.7620 (t0) cc_final: 0.7194 (t0) REVERT: B 201 TYR cc_start: 0.6750 (t80) cc_final: 0.6533 (t80) REVERT: E 91 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7917 (pp30) REVERT: E 107 GLU cc_start: 0.8372 (pm20) cc_final: 0.8060 (pm20) REVERT: F 111 ARG cc_start: 0.7526 (mmp-170) cc_final: 0.7098 (mmp-170) outliers start: 34 outliers final: 22 residues processed: 230 average time/residue: 0.2058 time to fit residues: 67.1615 Evaluate side-chains 221 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 197 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 95 TRP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 212 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 30.0000 chunk 51 optimal weight: 0.0970 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 102 GLN D 188 GLN ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 10698 Z= 0.442 Angle : 0.710 10.491 14562 Z= 0.360 Chirality : 0.045 0.163 1694 Planarity : 0.004 0.049 1834 Dihedral : 4.678 18.558 1466 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.75 % Favored : 91.73 % Rotamer: Outliers : 3.49 % Allowed : 20.51 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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: -1.28 (0.23), residues: 1342 helix: 0.43 (0.26), residues: 394 sheet: -1.54 (0.26), residues: 374 loop : -1.14 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 50 HIS 0.004 0.001 HIS F 112 PHE 0.024 0.002 PHE C 141 TYR 0.032 0.002 TYR E 142 ARG 0.005 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 218 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ILE cc_start: 0.9294 (mm) cc_final: 0.9075 (mt) REVERT: C 91 GLN cc_start: 0.8456 (pp30) cc_final: 0.7932 (pp30) REVERT: C 107 GLU cc_start: 0.8408 (pm20) cc_final: 0.7927 (pm20) REVERT: D 92 GLU cc_start: 0.8006 (tp30) cc_final: 0.7771 (tp30) REVERT: D 168 THR cc_start: 0.7024 (OUTLIER) cc_final: 0.6703 (p) REVERT: B 58 ASN cc_start: 0.7686 (t0) cc_final: 0.7280 (t0) REVERT: E 91 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8118 (pp30) REVERT: F 104 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.6352 (m-10) outliers start: 40 outliers final: 27 residues processed: 243 average time/residue: 0.2102 time to fit residues: 71.9488 Evaluate side-chains 233 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 203 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 95 TRP Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 104 TYR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 212 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.5437 > 50: distance: 10 - 30: 7.673 distance: 14 - 37: 10.623 distance: 24 - 30: 7.829 distance: 30 - 31: 19.067 distance: 31 - 32: 35.795 distance: 31 - 34: 12.749 distance: 32 - 33: 7.350 distance: 32 - 37: 27.747 distance: 34 - 35: 8.333 distance: 34 - 36: 22.016 distance: 37 - 38: 12.310 distance: 38 - 39: 13.225 distance: 38 - 41: 11.977 distance: 39 - 40: 31.746 distance: 39 - 45: 27.243 distance: 41 - 42: 16.482 distance: 42 - 43: 13.530 distance: 42 - 44: 42.401 distance: 45 - 46: 11.122 distance: 46 - 47: 33.443 distance: 46 - 49: 9.948 distance: 47 - 48: 21.492 distance: 47 - 50: 9.178 distance: 48 - 73: 41.185 distance: 50 - 51: 11.989 distance: 51 - 52: 25.634 distance: 51 - 54: 16.582 distance: 52 - 53: 18.357 distance: 52 - 58: 25.012 distance: 53 - 81: 19.432 distance: 54 - 55: 29.758 distance: 55 - 56: 13.411 distance: 55 - 57: 16.352 distance: 58 - 59: 31.902 distance: 59 - 60: 32.926 distance: 59 - 62: 18.678 distance: 60 - 61: 25.934 distance: 60 - 65: 6.213 distance: 62 - 63: 8.769 distance: 62 - 64: 32.457 distance: 65 - 66: 19.439 distance: 66 - 67: 19.894 distance: 66 - 69: 3.822 distance: 67 - 68: 11.283 distance: 68 - 99: 36.549 distance: 69 - 70: 3.508 distance: 70 - 71: 28.874 distance: 70 - 72: 14.344 distance: 73 - 74: 8.945 distance: 74 - 75: 24.231 distance: 74 - 77: 17.082 distance: 75 - 76: 14.820 distance: 75 - 81: 8.668 distance: 76 - 110: 10.266 distance: 77 - 78: 25.319 distance: 78 - 79: 17.394 distance: 78 - 80: 14.482 distance: 81 - 82: 8.834 distance: 82 - 83: 24.177 distance: 82 - 85: 26.164 distance: 83 - 84: 9.196 distance: 83 - 90: 20.516 distance: 84 - 115: 17.925 distance: 85 - 86: 19.134 distance: 86 - 87: 6.496 distance: 87 - 88: 8.636 distance: 87 - 89: 11.818 distance: 90 - 91: 5.532 distance: 91 - 92: 19.490 distance: 91 - 94: 6.626 distance: 92 - 93: 19.368 distance: 92 - 99: 23.272 distance: 93 - 123: 28.749 distance: 94 - 95: 3.591 distance: 95 - 96: 8.062 distance: 96 - 97: 26.307 distance: 97 - 98: 18.182 distance: 99 - 100: 20.641 distance: 100 - 101: 29.675 distance: 100 - 103: 35.163 distance: 101 - 102: 24.548 distance: 101 - 110: 20.634 distance: 103 - 104: 15.093 distance: 104 - 105: 24.655 distance: 105 - 106: 5.874 distance: 106 - 107: 18.769 distance: 107 - 108: 22.288 distance: 107 - 109: 20.473