Starting phenix.real_space_refine on Sun Mar 17 08:21:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4n_36887/03_2024/8k4n_36887_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4n_36887/03_2024/8k4n_36887.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4n_36887/03_2024/8k4n_36887_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4n_36887/03_2024/8k4n_36887_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4n_36887/03_2024/8k4n_36887_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4n_36887/03_2024/8k4n_36887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4n_36887/03_2024/8k4n_36887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4n_36887/03_2024/8k4n_36887_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4n_36887/03_2024/8k4n_36887_trim_updated.pdb" } resolution = 2.83 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 60 5.16 5 C 5543 2.51 5 N 1481 2.21 5 O 1571 1.98 5 H 8511 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 36": "OD1" <-> "OD2" Residue "E ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 208": "OE1" <-> "OE2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 286": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17167 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3310 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 4984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 4984 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 759 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3417 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 4666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4666 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 4, 'TRANS': 274} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'VF0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.72, per 1000 atoms: 0.45 Number of scatterers: 17167 At special positions: 0 Unit cell: (91.8, 119.85, 132.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 1 15.00 O 1571 8.00 N 1481 7.00 C 5543 6.00 H 8511 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 204 " 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: 12.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 12 sheets defined 27.0% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.917A pdb=" N GLU A 14 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG A 15 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 17 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 19 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 20 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG A 21 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 23 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 24 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 28 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 29 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 30 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 274 No H-bonds generated for 'chain 'A' and resid 271 through 274' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.414A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.581A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 21 removed outlier: 3.986A pdb=" N GLU B 10 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA B 11 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 13 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'D' and resid 56 through 80 removed outlier: 4.391A pdb=" N VAL D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 106 Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.843A pdb=" N TYR D 113 " --> pdb=" O PHE D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 138 removed outlier: 4.144A pdb=" N THR D 132 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU D 133 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 154 removed outlier: 4.356A pdb=" N LEU D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 193 removed outlier: 3.603A pdb=" N VAL D 174 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP D 179 " --> pdb=" O CYS D 175 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU D 183 " --> pdb=" O TRP D 179 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 238 removed outlier: 3.773A pdb=" N PHE D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 232 " --> pdb=" O TRP D 228 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 243 No H-bonds generated for 'chain 'D' and resid 240 through 243' Processing helix chain 'D' and resid 248 through 251 No H-bonds generated for 'chain 'D' and resid 248 through 251' Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 270 through 279 removed outlier: 3.964A pdb=" N PHE D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 293 removed outlier: 4.253A pdb=" N ILE D 290 " --> pdb=" O PHE D 287 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER D 291 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER D 292 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN D 293 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 319 removed outlier: 4.083A pdb=" N HIS D 306 " --> pdb=" O LYS D 302 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE D 311 " --> pdb=" O LYS D 307 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.514A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.992A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.993A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.598A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.679A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 250 through 254 Processing sheet with id= G, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.507A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.813A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 4 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 3.722A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 143 through 147 Processing sheet with id= L, first strand: chain 'E' and resid 231 through 233 removed outlier: 6.202A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 292 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.06 Time building geometry restraints manager: 12.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8484 1.03 - 1.23: 32 1.23 - 1.42: 3729 1.42 - 1.62: 5010 1.62 - 1.81: 89 Bond restraints: 17344 Sorted by residual: bond pdb=" C09 VF0 D 401 " pdb=" C10 VF0 D 401 " ideal model delta sigma weight residual 1.317 1.525 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" O28 VF0 D 401 " pdb=" P26 VF0 D 401 " ideal model delta sigma weight residual 1.510 1.456 0.054 2.00e-02 2.50e+03 7.21e+00 bond pdb=" O27 VF0 D 401 " pdb=" P26 VF0 D 401 " ideal model delta sigma weight residual 1.510 1.459 0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" CB ARG E 38 " pdb=" CG ARG E 38 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.54e+00 bond pdb=" CB ILE B 232 " pdb=" CG2 ILE B 232 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.03e+00 ... (remaining 17339 not shown) Histogram of bond angle deviations from ideal: 97.62 - 104.92: 97 104.92 - 112.22: 19556 112.22 - 119.51: 4319 119.51 - 126.81: 7112 126.81 - 134.10: 104 Bond angle restraints: 31188 Sorted by residual: angle pdb=" N VAL D 124 " pdb=" CA VAL D 124 " pdb=" C VAL D 124 " ideal model delta sigma weight residual 113.71 108.45 5.26 9.50e-01 1.11e+00 3.07e+01 angle pdb=" N ALA E 92 " pdb=" CA ALA E 92 " pdb=" C ALA E 92 " ideal model delta sigma weight residual 107.88 113.52 -5.64 1.41e+00 5.03e-01 1.60e+01 angle pdb=" N ILE A 19 " pdb=" CA ILE A 19 " pdb=" C ILE A 19 " ideal model delta sigma weight residual 111.67 108.19 3.48 9.50e-01 1.11e+00 1.34e+01 angle pdb=" C09 VF0 D 401 " pdb=" C10 VF0 D 401 " pdb=" C11 VF0 D 401 " ideal model delta sigma weight residual 120.00 109.37 10.63 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C08 VF0 D 401 " pdb=" C09 VF0 D 401 " pdb=" C10 VF0 D 401 " ideal model delta sigma weight residual 120.00 110.63 9.37 3.00e+00 1.11e-01 9.75e+00 ... (remaining 31183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.29: 7892 30.29 - 60.58: 297 60.58 - 90.86: 9 90.86 - 121.15: 1 121.15 - 151.44: 1 Dihedral angle restraints: 8200 sinusoidal: 4320 harmonic: 3880 Sorted by residual: dihedral pdb=" CA SER D 292 " pdb=" C SER D 292 " pdb=" N GLN D 293 " pdb=" CA GLN D 293 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CB CYS D 127 " pdb=" SG CYS D 127 " pdb=" SG CYS D 204 " pdb=" CB CYS D 204 " ideal model delta sinusoidal sigma weight residual 93.00 131.66 -38.66 1 1.00e+01 1.00e-02 2.10e+01 ... (remaining 8197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 800 0.038 - 0.075: 409 0.075 - 0.113: 142 0.113 - 0.151: 20 0.151 - 0.188: 3 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CB VAL A 218 " pdb=" CA VAL A 218 " pdb=" CG1 VAL A 218 " pdb=" CG2 VAL A 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CB VAL A 34 " pdb=" CA VAL A 34 " pdb=" CG1 VAL A 34 " pdb=" CG2 VAL A 34 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CB VAL B 112 " pdb=" CA VAL B 112 " pdb=" CG1 VAL B 112 " pdb=" CG2 VAL B 112 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 1371 not shown) Planarity restraints: 2576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 VF0 D 401 " 0.307 2.00e-02 2.50e+03 3.01e-01 9.08e+02 pdb=" C09 VF0 D 401 " -0.324 2.00e-02 2.50e+03 pdb=" C10 VF0 D 401 " -0.277 2.00e-02 2.50e+03 pdb=" C11 VF0 D 401 " 0.295 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO E 107 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 107 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.93e+00 pdb=" N PRO D 108 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 108 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 108 " -0.019 5.00e-02 4.00e+02 ... (remaining 2573 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 454 2.11 - 2.73: 30358 2.73 - 3.36: 44862 3.36 - 3.98: 59946 3.98 - 4.60: 96311 Nonbonded interactions: 231931 Sorted by model distance: nonbonded pdb=" O THR B 29 " pdb=" H GLN B 32 " model vdw 1.488 1.850 nonbonded pdb=" OE1 GLU E 6 " pdb=" H GLY E 114 " model vdw 1.610 1.850 nonbonded pdb=" HG1 THR B 34 " pdb=" O LEU B 300 " model vdw 1.631 1.850 nonbonded pdb=" O GLY D 68 " pdb="HD21 ASN D 72 " model vdw 1.641 1.850 nonbonded pdb=" O LYS B 57 " pdb=" HG SER B 74 " model vdw 1.651 1.850 ... (remaining 231926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 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: 0.250 Extract box with map and model: 13.580 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 55.160 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.009 0.208 8833 Z= 0.603 Angle : 0.691 10.633 11958 Z= 0.382 Chirality : 0.047 0.188 1374 Planarity : 0.009 0.301 1492 Dihedral : 14.409 151.440 3122 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -4.19 (0.21), residues: 1101 helix: -3.40 (0.21), residues: 343 sheet: -0.93 (0.30), residues: 282 loop : -3.42 (0.21), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.007 0.001 HIS E 35 PHE 0.018 0.002 PHE B 151 TYR 0.023 0.002 TYR E 178 ARG 0.008 0.001 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASP cc_start: 0.6902 (p0) cc_final: 0.6653 (p0) REVERT: B 325 MET cc_start: 0.7449 (mmt) cc_final: 0.7212 (mmt) REVERT: E 43 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7719 (ttpt) REVERT: D 195 LYS cc_start: 0.4766 (mmtp) cc_final: 0.4195 (ptpp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 2.4303 time to fit residues: 422.0024 Evaluate side-chains 132 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 0.0060 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 156 GLN B 175 GLN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 167 GLN D 116 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8833 Z= 0.156 Angle : 0.494 4.583 11958 Z= 0.268 Chirality : 0.040 0.138 1374 Planarity : 0.003 0.037 1492 Dihedral : 7.322 129.561 1224 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.31 % Allowed : 13.44 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -3.03 (0.23), residues: 1101 helix: -2.35 (0.24), residues: 350 sheet: -0.47 (0.31), residues: 282 loop : -2.66 (0.24), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS D 114 PHE 0.013 0.001 PHE D 109 TYR 0.010 0.001 TYR D 327 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 13 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6974 (mm-40) REVERT: E 43 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7629 (ttpt) REVERT: E 182 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8328 (m110) REVERT: D 169 LYS cc_start: 0.7155 (tptp) cc_final: 0.6756 (tptt) REVERT: D 195 LYS cc_start: 0.4817 (mmtp) cc_final: 0.4240 (ptpp) outliers start: 12 outliers final: 4 residues processed: 152 average time/residue: 2.1442 time to fit residues: 351.3379 Evaluate side-chains 137 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 0.0770 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN C 59 ASN D 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8833 Z= 0.219 Angle : 0.521 7.474 11958 Z= 0.280 Chirality : 0.041 0.137 1374 Planarity : 0.003 0.036 1492 Dihedral : 6.678 106.910 1224 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.53 % Allowed : 15.30 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.48 (0.23), residues: 1101 helix: -1.85 (0.26), residues: 344 sheet: -0.24 (0.31), residues: 282 loop : -2.32 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE D 227 TYR 0.012 0.001 TYR D 207 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8613 (pt) REVERT: E 182 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8288 (m110) REVERT: D 109 PHE cc_start: 0.7337 (m-10) cc_final: 0.7133 (m-80) REVERT: D 195 LYS cc_start: 0.4903 (mmtp) cc_final: 0.4444 (ptmm) REVERT: D 319 ASN cc_start: 0.8328 (t0) cc_final: 0.8085 (t0) outliers start: 14 outliers final: 9 residues processed: 146 average time/residue: 2.0959 time to fit residues: 330.8759 Evaluate side-chains 142 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 47 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 ASN D 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8833 Z= 0.193 Angle : 0.490 4.254 11958 Z= 0.265 Chirality : 0.040 0.139 1374 Planarity : 0.003 0.035 1492 Dihedral : 6.311 90.446 1224 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.64 % Allowed : 16.83 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.20 (0.24), residues: 1101 helix: -1.64 (0.26), residues: 350 sheet: -0.10 (0.31), residues: 281 loop : -2.10 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE D 227 TYR 0.011 0.001 TYR D 207 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8618 (pt) REVERT: E 13 GLN cc_start: 0.7216 (mm-40) cc_final: 0.6932 (mm-40) REVERT: D 109 PHE cc_start: 0.7410 (m-10) cc_final: 0.7166 (m-80) REVERT: D 195 LYS cc_start: 0.4961 (mmtp) cc_final: 0.4544 (ptmm) REVERT: D 319 ASN cc_start: 0.8346 (t0) cc_final: 0.8103 (t0) outliers start: 15 outliers final: 10 residues processed: 148 average time/residue: 2.2112 time to fit residues: 351.9620 Evaluate side-chains 146 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 59 ASN E 113 GLN D 116 ASN D 157 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8833 Z= 0.175 Angle : 0.472 4.767 11958 Z= 0.255 Chirality : 0.040 0.132 1374 Planarity : 0.003 0.035 1492 Dihedral : 5.958 73.360 1224 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.75 % Allowed : 17.70 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.91 (0.24), residues: 1101 helix: -1.41 (0.27), residues: 350 sheet: 0.01 (0.31), residues: 280 loop : -1.88 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE D 227 TYR 0.012 0.001 TYR D 113 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 13 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6934 (mm-40) REVERT: D 195 LYS cc_start: 0.4879 (mmtp) cc_final: 0.4541 (ptmm) REVERT: D 319 ASN cc_start: 0.8311 (t0) cc_final: 0.8069 (t0) outliers start: 16 outliers final: 10 residues processed: 147 average time/residue: 2.2426 time to fit residues: 354.3873 Evaluate side-chains 144 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN D 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8833 Z= 0.199 Angle : 0.488 5.041 11958 Z= 0.263 Chirality : 0.040 0.133 1374 Planarity : 0.003 0.034 1492 Dihedral : 5.871 63.964 1224 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.19 % Allowed : 17.92 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.72 (0.24), residues: 1101 helix: -1.25 (0.27), residues: 349 sheet: 0.11 (0.31), residues: 282 loop : -1.77 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE D 227 TYR 0.016 0.001 TYR D 113 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6937 (mm-40) REVERT: D 195 LYS cc_start: 0.5000 (mmtp) cc_final: 0.4662 (ptmm) REVERT: D 319 ASN cc_start: 0.8372 (t0) cc_final: 0.8118 (t0) outliers start: 20 outliers final: 13 residues processed: 153 average time/residue: 2.3507 time to fit residues: 386.1426 Evaluate side-chains 147 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN D 116 ASN D 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8833 Z= 0.170 Angle : 0.469 5.021 11958 Z= 0.252 Chirality : 0.040 0.133 1374 Planarity : 0.003 0.057 1492 Dihedral : 5.667 54.738 1224 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.97 % Allowed : 19.89 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.53 (0.24), residues: 1101 helix: -1.10 (0.27), residues: 349 sheet: 0.15 (0.31), residues: 282 loop : -1.60 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE D 227 TYR 0.019 0.001 TYR D 113 ARG 0.004 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 33 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7885 (mt) REVERT: B 70 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8512 (pt) REVERT: E 13 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6906 (mm-40) REVERT: D 195 LYS cc_start: 0.4971 (mmtp) cc_final: 0.4660 (ptmm) REVERT: D 319 ASN cc_start: 0.8308 (t0) cc_final: 0.8044 (t0) outliers start: 18 outliers final: 12 residues processed: 145 average time/residue: 2.1532 time to fit residues: 336.6563 Evaluate side-chains 144 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 193 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN D 116 ASN D 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8833 Z= 0.178 Angle : 0.473 4.936 11958 Z= 0.255 Chirality : 0.040 0.130 1374 Planarity : 0.003 0.035 1492 Dihedral : 5.554 54.889 1224 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.40 % Allowed : 19.78 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.41 (0.25), residues: 1101 helix: -0.98 (0.28), residues: 348 sheet: 0.17 (0.31), residues: 288 loop : -1.52 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE D 227 TYR 0.021 0.001 TYR D 113 ARG 0.005 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.7895 (p) REVERT: A 308 GLU cc_start: 0.8081 (tt0) cc_final: 0.7724 (tt0) REVERT: B 33 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7922 (mt) REVERT: B 70 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8521 (pt) REVERT: E 13 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6899 (mm-40) REVERT: D 195 LYS cc_start: 0.4856 (mmtp) cc_final: 0.4523 (ptmm) REVERT: D 319 ASN cc_start: 0.8350 (t0) cc_final: 0.8080 (t0) outliers start: 22 outliers final: 14 residues processed: 143 average time/residue: 2.1982 time to fit residues: 338.2967 Evaluate side-chains 144 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 92 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN D 116 ASN D 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8833 Z= 0.178 Angle : 0.476 5.875 11958 Z= 0.256 Chirality : 0.040 0.133 1374 Planarity : 0.003 0.047 1492 Dihedral : 5.307 53.688 1224 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.19 % Allowed : 19.67 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.26 (0.25), residues: 1101 helix: -0.87 (0.28), residues: 347 sheet: 0.21 (0.31), residues: 288 loop : -1.39 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE D 227 TYR 0.020 0.001 TYR D 113 ARG 0.008 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.7884 (p) REVERT: B 70 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8517 (pt) REVERT: E 13 GLN cc_start: 0.7187 (mm-40) cc_final: 0.6878 (mm-40) REVERT: D 195 LYS cc_start: 0.4865 (mmtp) cc_final: 0.4525 (ptmm) REVERT: D 319 ASN cc_start: 0.8329 (t0) cc_final: 0.8057 (t0) outliers start: 20 outliers final: 16 residues processed: 144 average time/residue: 2.2814 time to fit residues: 352.7821 Evaluate side-chains 144 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN D 116 ASN D 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8833 Z= 0.229 Angle : 0.507 6.532 11958 Z= 0.273 Chirality : 0.041 0.132 1374 Planarity : 0.003 0.045 1492 Dihedral : 5.392 52.912 1224 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.19 % Allowed : 20.00 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1101 helix: -0.87 (0.28), residues: 348 sheet: 0.20 (0.31), residues: 288 loop : -1.41 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE D 227 TYR 0.020 0.001 TYR D 113 ARG 0.007 0.000 ARG D 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.7912 (p) REVERT: B 33 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7975 (mt) REVERT: B 70 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8588 (pt) REVERT: D 195 LYS cc_start: 0.4846 (mmtp) cc_final: 0.4458 (ptmm) REVERT: D 319 ASN cc_start: 0.8368 (t0) cc_final: 0.8099 (t0) outliers start: 20 outliers final: 14 residues processed: 142 average time/residue: 2.3122 time to fit residues: 353.3294 Evaluate side-chains 140 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN D 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.108735 restraints weight = 30203.569| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.20 r_work: 0.3091 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8833 Z= 0.213 Angle : 0.505 6.065 11958 Z= 0.270 Chirality : 0.041 0.133 1374 Planarity : 0.003 0.042 1492 Dihedral : 5.389 54.371 1224 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.30 % Allowed : 20.33 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.18 (0.25), residues: 1101 helix: -0.79 (0.28), residues: 349 sheet: 0.22 (0.31), residues: 288 loop : -1.33 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE D 227 TYR 0.020 0.001 TYR D 113 ARG 0.006 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6983.99 seconds wall clock time: 122 minutes 37.35 seconds (7357.35 seconds total)