Starting phenix.real_space_refine on Wed Feb 12 16:05:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y62_38964/02_2025/8y62_38964.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y62_38964/02_2025/8y62_38964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y62_38964/02_2025/8y62_38964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y62_38964/02_2025/8y62_38964.map" model { file = "/net/cci-nas-00/data/ceres_data/8y62_38964/02_2025/8y62_38964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y62_38964/02_2025/8y62_38964.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5244 2.51 5 N 1393 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8160 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1593 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2474 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 86 Chain: "C" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 337 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "E" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1687 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "R" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2031 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'16C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.80, per 1000 atoms: 0.59 Number of scatterers: 8160 At special positions: 0 Unit cell: (87.98, 119.78, 126.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1470 8.00 N 1393 7.00 C 5244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 38.8% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.798A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.385A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.780A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 244 through 255 removed outlier: 3.515A pdb=" N ASP A 251 " --> pdb=" O MET A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.047A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 6 through 26 removed outlier: 4.234A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 10 through 23 removed outlier: 3.806A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.529A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.850A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.919A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 51 removed outlier: 3.516A pdb=" N VAL R 35 " --> pdb=" O VAL R 31 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TRP R 49 " --> pdb=" O GLY R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 88 Proline residue: R 79 - end of helix Processing helix chain 'R' and resid 94 through 129 removed outlier: 3.633A pdb=" N VAL R 113 " --> pdb=" O LEU R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 136 Processing helix chain 'R' and resid 138 through 163 removed outlier: 4.027A pdb=" N VAL R 147 " --> pdb=" O MET R 143 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY R 148 " --> pdb=" O LYS R 144 " (cutoff:3.500A) Proline residue: R 149 - end of helix Proline residue: R 159 - end of helix removed outlier: 3.877A pdb=" N LEU R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 209 removed outlier: 3.732A pdb=" N LEU R 191 " --> pdb=" O PRO R 187 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS R 192 " --> pdb=" O GLU R 188 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL R 193 " --> pdb=" O GLU R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 231 Processing helix chain 'R' and resid 238 through 275 removed outlier: 5.395A pdb=" N THR R 244 " --> pdb=" O LEU R 240 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N CYS R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) Proline residue: R 256 - end of helix removed outlier: 5.235A pdb=" N LYS R 269 " --> pdb=" O THR R 265 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLU R 270 " --> pdb=" O VAL R 266 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE R 273 " --> pdb=" O LYS R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 283 Processing helix chain 'R' and resid 283 through 303 removed outlier: 3.757A pdb=" N ASN R 294 " --> pdb=" O LEU R 290 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 317 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.648A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.713A 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: 7.229A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 50 removed outlier: 3.744A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.773A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.010A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.929A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.614A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.567A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.688A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.664A pdb=" N THR E 69 " --> pdb=" O GLN E 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.174A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.758A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.545A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.916A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 164 through 166 removed outlier: 3.619A pdb=" N THR R 177 " --> pdb=" O THR R 165 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1107 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: 2.28 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1287 1.31 - 1.43: 2341 1.43 - 1.56: 4632 1.56 - 1.68: 1 1.68 - 1.81: 76 Bond restraints: 8337 Sorted by residual: bond pdb=" C19 16C R 401 " pdb=" N2 16C R 401 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" CA SER E 23 " pdb=" C SER E 23 " ideal model delta sigma weight residual 1.525 1.484 0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" C ARG A 24 " pdb=" O ARG A 24 " ideal model delta sigma weight residual 1.237 1.203 0.033 1.16e-02 7.43e+03 8.23e+00 bond pdb=" CA ARG A 24 " pdb=" C ARG A 24 " ideal model delta sigma weight residual 1.524 1.490 0.033 1.26e-02 6.30e+03 7.06e+00 bond pdb=" CA CYS E 22 " pdb=" CB CYS E 22 " ideal model delta sigma weight residual 1.530 1.491 0.040 1.50e-02 4.44e+03 6.98e+00 ... (remaining 8332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11074 1.92 - 3.83: 241 3.83 - 5.75: 48 5.75 - 7.66: 5 7.66 - 9.58: 3 Bond angle restraints: 11371 Sorted by residual: angle pdb=" N CYS R 253 " pdb=" CA CYS R 253 " pdb=" C CYS R 253 " ideal model delta sigma weight residual 113.23 119.24 -6.01 1.24e+00 6.50e-01 2.35e+01 angle pdb=" N LYS A 46 " pdb=" CA LYS A 46 " pdb=" C LYS A 46 " ideal model delta sigma weight residual 112.23 106.20 6.03 1.26e+00 6.30e-01 2.29e+01 angle pdb=" C ILE R 252 " pdb=" CA ILE R 252 " pdb=" CB ILE R 252 " ideal model delta sigma weight residual 112.05 117.33 -5.28 1.46e+00 4.69e-01 1.31e+01 angle pdb=" N ALA B 140 " pdb=" CA ALA B 140 " pdb=" C ALA B 140 " ideal model delta sigma weight residual 109.52 114.67 -5.15 1.55e+00 4.16e-01 1.10e+01 angle pdb=" C GLU E 234 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " ideal model delta sigma weight residual 121.80 113.70 8.10 2.44e+00 1.68e-01 1.10e+01 ... (remaining 11366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.36: 4585 24.36 - 48.72: 228 48.72 - 73.09: 16 73.09 - 97.45: 6 97.45 - 121.81: 1 Dihedral angle restraints: 4836 sinusoidal: 1589 harmonic: 3247 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual -86.00 -134.20 48.20 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" CA LEU R 240 " pdb=" C LEU R 240 " pdb=" N ARG R 241 " pdb=" CA ARG R 241 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ALA A 7 " pdb=" C ALA A 7 " pdb=" N GLU A 8 " pdb=" CA GLU A 8 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 4833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 942 0.045 - 0.089: 315 0.089 - 0.134: 80 0.134 - 0.178: 9 0.178 - 0.223: 3 Chirality restraints: 1349 Sorted by residual: chirality pdb=" C3 16C R 401 " pdb=" C2 16C R 401 " pdb=" C4 16C R 401 " pdb=" O3 16C R 401 " both_signs ideal model delta sigma weight residual False -2.28 -2.51 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ARG E 191 " pdb=" N ARG E 191 " pdb=" C ARG E 191 " pdb=" CB ARG E 191 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE R 252 " pdb=" N ILE R 252 " pdb=" C ILE R 252 " pdb=" CB ILE R 252 " both_signs ideal model delta sigma weight residual False 2.43 2.25 0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 1346 not shown) Planarity restraints: 1435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 281 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO A 282 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 52 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO C 53 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " -0.028 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO C 49 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " -0.024 5.00e-02 4.00e+02 ... (remaining 1432 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1019 2.74 - 3.28: 8052 3.28 - 3.82: 13016 3.82 - 4.36: 14491 4.36 - 4.90: 25556 Nonbonded interactions: 62134 Sorted by model distance: nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.232 3.040 nonbonded pdb=" OG SER E 204 " pdb=" OG1 THR E 215 " model vdw 2.272 3.040 nonbonded pdb=" O MET A 243 " pdb=" OG SER A 246 " model vdw 2.274 3.040 nonbonded pdb=" NH1 ARG R 123 " pdb=" OH TYR R 221 " model vdw 2.289 3.120 ... (remaining 62129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.490 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 : 0.006 0.105 8337 Z= 0.376 Angle : 0.726 9.578 11371 Z= 0.400 Chirality : 0.047 0.223 1349 Planarity : 0.004 0.055 1435 Dihedral : 13.806 121.810 2734 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.13 % Allowed : 0.65 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.26), residues: 1110 helix: 0.42 (0.27), residues: 389 sheet: -1.68 (0.33), residues: 254 loop : -1.72 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 36 HIS 0.009 0.001 HIS B 183 PHE 0.017 0.002 PHE A 307 TYR 0.023 0.002 TYR E 235 ARG 0.020 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.842 Fit side-chains REVERT: A 20 ASP cc_start: 0.8003 (t0) cc_final: 0.7728 (t0) REVERT: A 206 SER cc_start: 0.8377 (t) cc_final: 0.8166 (t) REVERT: A 247 MET cc_start: 0.8846 (ttt) cc_final: 0.8427 (ttt) REVERT: A 255 ASN cc_start: 0.8850 (m-40) cc_final: 0.8283 (m-40) REVERT: A 257 LYS cc_start: 0.8818 (ptmm) cc_final: 0.8385 (ttpp) REVERT: A 274 PHE cc_start: 0.8876 (t80) cc_final: 0.8091 (t80) REVERT: A 337 ASP cc_start: 0.8455 (t70) cc_final: 0.8171 (t0) REVERT: A 350 ASP cc_start: 0.8692 (t0) cc_final: 0.8288 (t0) REVERT: B 261 LEU cc_start: 0.8887 (mp) cc_final: 0.8623 (mp) REVERT: B 275 SER cc_start: 0.8788 (m) cc_final: 0.8567 (m) REVERT: E 52 SER cc_start: 0.8333 (t) cc_final: 0.7982 (t) REVERT: E 83 MET cc_start: 0.8605 (mmp) cc_final: 0.8243 (mmp) REVERT: R 80 PHE cc_start: 0.8758 (m-10) cc_final: 0.8513 (m-10) REVERT: R 203 ILE cc_start: 0.8582 (tp) cc_final: 0.8351 (tp) REVERT: R 262 LEU cc_start: 0.9190 (tp) cc_final: 0.8877 (tp) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.2344 time to fit residues: 75.7257 Evaluate side-chains 222 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 0.0970 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.2980 chunk 100 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.082836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.072134 restraints weight = 17412.814| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.83 r_work: 0.2870 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8337 Z= 0.194 Angle : 0.602 11.617 11371 Z= 0.310 Chirality : 0.043 0.143 1349 Planarity : 0.004 0.037 1435 Dihedral : 7.159 118.971 1230 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.44 % Allowed : 11.49 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.26), residues: 1110 helix: 0.97 (0.27), residues: 390 sheet: -1.53 (0.31), residues: 258 loop : -1.52 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.006 0.001 HIS B 183 PHE 0.013 0.001 PHE R 309 TYR 0.017 0.001 TYR E 235 ARG 0.006 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 231 time to evaluate : 0.988 Fit side-chains REVERT: A 20 ASP cc_start: 0.8249 (t0) cc_final: 0.7999 (t0) REVERT: A 255 ASN cc_start: 0.9001 (m-40) cc_final: 0.8292 (m-40) REVERT: A 257 LYS cc_start: 0.8943 (ptmm) cc_final: 0.8470 (ptmm) REVERT: A 274 PHE cc_start: 0.9019 (t80) cc_final: 0.8473 (t80) REVERT: A 337 ASP cc_start: 0.8708 (t70) cc_final: 0.8455 (t0) REVERT: A 345 LYS cc_start: 0.8771 (tppt) cc_final: 0.8287 (mppt) REVERT: A 350 ASP cc_start: 0.8984 (t0) cc_final: 0.8605 (t0) REVERT: B 14 LEU cc_start: 0.9451 (mm) cc_final: 0.9096 (mp) REVERT: B 49 ARG cc_start: 0.8715 (mmm-85) cc_final: 0.8501 (mmm-85) REVERT: B 148 CYS cc_start: 0.8804 (t) cc_final: 0.8516 (t) REVERT: B 247 ASP cc_start: 0.8512 (p0) cc_final: 0.8243 (p0) REVERT: B 261 LEU cc_start: 0.9092 (mp) cc_final: 0.8842 (mp) REVERT: B 275 SER cc_start: 0.8883 (m) cc_final: 0.8669 (m) REVERT: E 39 GLN cc_start: 0.8991 (tt0) cc_final: 0.8686 (tt0) REVERT: E 81 LEU cc_start: 0.8146 (tp) cc_final: 0.7888 (tt) REVERT: E 83 MET cc_start: 0.8283 (mmp) cc_final: 0.7901 (mmp) REVERT: E 93 MET cc_start: 0.7814 (tmm) cc_final: 0.7554 (tmm) REVERT: E 210 THR cc_start: 0.9218 (m) cc_final: 0.8987 (m) REVERT: R 214 MET cc_start: 0.8439 (tpp) cc_final: 0.7827 (tpt) REVERT: R 262 LEU cc_start: 0.9151 (tp) cc_final: 0.8842 (tp) REVERT: R 294 ASN cc_start: 0.8734 (t0) cc_final: 0.8332 (t0) REVERT: R 312 ARG cc_start: 0.8750 (tpp80) cc_final: 0.8438 (tpp80) outliers start: 11 outliers final: 5 residues processed: 237 average time/residue: 0.2293 time to fit residues: 71.9256 Evaluate side-chains 220 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 215 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 263 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.081665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.070853 restraints weight = 17897.181| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.84 r_work: 0.2850 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8337 Z= 0.237 Angle : 0.588 11.289 11371 Z= 0.300 Chirality : 0.042 0.142 1349 Planarity : 0.004 0.037 1435 Dihedral : 7.052 118.400 1230 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.87 % Allowed : 14.23 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.26), residues: 1110 helix: 1.10 (0.27), residues: 390 sheet: -1.33 (0.31), residues: 264 loop : -1.40 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.007 0.001 HIS B 183 PHE 0.011 0.001 PHE B 292 TYR 0.015 0.001 TYR E 235 ARG 0.008 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.719 Fit side-chains REVERT: A 20 ASP cc_start: 0.8300 (t0) cc_final: 0.8018 (t0) REVERT: A 255 ASN cc_start: 0.9047 (m-40) cc_final: 0.8322 (m-40) REVERT: A 274 PHE cc_start: 0.9042 (t80) cc_final: 0.8538 (t80) REVERT: A 337 ASP cc_start: 0.8743 (t70) cc_final: 0.8486 (t0) REVERT: A 350 ASP cc_start: 0.9002 (t0) cc_final: 0.8643 (t0) REVERT: B 217 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8611 (ptp) REVERT: B 228 ASP cc_start: 0.7863 (p0) cc_final: 0.7485 (p0) REVERT: B 247 ASP cc_start: 0.8577 (p0) cc_final: 0.8253 (p0) REVERT: B 261 LEU cc_start: 0.9121 (mp) cc_final: 0.8865 (mp) REVERT: B 275 SER cc_start: 0.8907 (m) cc_final: 0.8704 (m) REVERT: E 39 GLN cc_start: 0.8985 (tt0) cc_final: 0.8717 (tt0) REVERT: E 83 MET cc_start: 0.8213 (mmp) cc_final: 0.7846 (mmp) REVERT: E 93 MET cc_start: 0.7822 (tmm) cc_final: 0.7425 (tmm) REVERT: E 210 THR cc_start: 0.9186 (m) cc_final: 0.8957 (m) REVERT: R 214 MET cc_start: 0.8515 (tpp) cc_final: 0.8113 (tpt) REVERT: R 262 LEU cc_start: 0.9095 (tp) cc_final: 0.8797 (tp) REVERT: R 294 ASN cc_start: 0.8679 (t0) cc_final: 0.8333 (t0) outliers start: 22 outliers final: 16 residues processed: 231 average time/residue: 0.2257 time to fit residues: 68.3909 Evaluate side-chains 231 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 263 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 102 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.083543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.072754 restraints weight = 17613.492| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.83 r_work: 0.2888 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8337 Z= 0.151 Angle : 0.542 8.891 11371 Z= 0.277 Chirality : 0.042 0.137 1349 Planarity : 0.003 0.038 1435 Dihedral : 6.856 117.837 1230 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.74 % Allowed : 17.36 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.26), residues: 1110 helix: 1.45 (0.28), residues: 383 sheet: -0.99 (0.32), residues: 253 loop : -1.39 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 339 HIS 0.005 0.001 HIS B 183 PHE 0.017 0.001 PHE R 309 TYR 0.012 0.001 TYR E 235 ARG 0.009 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 0.849 Fit side-chains REVERT: A 8 GLU cc_start: 0.8516 (pm20) cc_final: 0.7842 (pm20) REVERT: A 20 ASP cc_start: 0.8285 (t0) cc_final: 0.7995 (t0) REVERT: A 255 ASN cc_start: 0.8979 (m-40) cc_final: 0.8300 (m-40) REVERT: A 274 PHE cc_start: 0.9038 (t80) cc_final: 0.8680 (t80) REVERT: A 337 ASP cc_start: 0.8716 (t70) cc_final: 0.8457 (t0) REVERT: A 350 ASP cc_start: 0.8931 (t0) cc_final: 0.8656 (t0) REVERT: B 217 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8540 (ptp) REVERT: B 228 ASP cc_start: 0.7780 (p0) cc_final: 0.7468 (p0) REVERT: B 261 LEU cc_start: 0.9128 (mp) cc_final: 0.8873 (mp) REVERT: B 275 SER cc_start: 0.8871 (m) cc_final: 0.8662 (m) REVERT: B 292 PHE cc_start: 0.8784 (m-10) cc_final: 0.8519 (m-10) REVERT: B 297 TRP cc_start: 0.8993 (m100) cc_final: 0.8655 (m100) REVERT: E 39 GLN cc_start: 0.8970 (tt0) cc_final: 0.8724 (tt0) REVERT: E 83 MET cc_start: 0.8067 (mmp) cc_final: 0.7686 (mmp) REVERT: E 93 MET cc_start: 0.7759 (tmm) cc_final: 0.7257 (tmm) REVERT: E 233 LEU cc_start: 0.9200 (tp) cc_final: 0.8876 (tp) REVERT: R 80 PHE cc_start: 0.8924 (m-10) cc_final: 0.8664 (m-10) REVERT: R 143 MET cc_start: 0.8746 (tpp) cc_final: 0.8445 (mpp) REVERT: R 214 MET cc_start: 0.8448 (tpp) cc_final: 0.8164 (tpt) REVERT: R 262 LEU cc_start: 0.9059 (tp) cc_final: 0.8712 (tp) outliers start: 21 outliers final: 15 residues processed: 232 average time/residue: 0.2306 time to fit residues: 69.7758 Evaluate side-chains 234 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 280 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 30 optimal weight: 0.2980 chunk 84 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN A 331 ASN B 36 ASN R 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.083390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.072662 restraints weight = 17716.556| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.83 r_work: 0.2886 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8337 Z= 0.170 Angle : 0.547 11.244 11371 Z= 0.277 Chirality : 0.041 0.141 1349 Planarity : 0.004 0.041 1435 Dihedral : 6.752 116.973 1230 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.39 % Allowed : 18.80 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1110 helix: 1.60 (0.28), residues: 383 sheet: -0.79 (0.33), residues: 253 loop : -1.32 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 339 HIS 0.006 0.001 HIS B 183 PHE 0.021 0.001 PHE B 222 TYR 0.011 0.001 TYR E 235 ARG 0.010 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.837 Fit side-chains REVERT: A 8 GLU cc_start: 0.8566 (pm20) cc_final: 0.7953 (pm20) REVERT: A 20 ASP cc_start: 0.8292 (t0) cc_final: 0.7908 (t0) REVERT: A 255 ASN cc_start: 0.9008 (m-40) cc_final: 0.8336 (m-40) REVERT: A 274 PHE cc_start: 0.9034 (t80) cc_final: 0.8688 (t80) REVERT: A 350 ASP cc_start: 0.8949 (t0) cc_final: 0.8687 (t0) REVERT: B 217 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8522 (ptp) REVERT: B 228 ASP cc_start: 0.7706 (p0) cc_final: 0.7385 (p0) REVERT: B 232 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8824 (tt) REVERT: B 261 LEU cc_start: 0.9137 (mp) cc_final: 0.8867 (mp) REVERT: B 292 PHE cc_start: 0.8840 (m-10) cc_final: 0.8587 (m-10) REVERT: B 297 TRP cc_start: 0.9004 (m100) cc_final: 0.8694 (m100) REVERT: B 316 SER cc_start: 0.9027 (t) cc_final: 0.8433 (p) REVERT: B 325 MET cc_start: 0.8934 (mtp) cc_final: 0.8617 (mtp) REVERT: E 52 SER cc_start: 0.8383 (t) cc_final: 0.7788 (p) REVERT: E 83 MET cc_start: 0.7959 (mmp) cc_final: 0.7569 (mmp) REVERT: E 93 MET cc_start: 0.7763 (tmm) cc_final: 0.7211 (tmm) REVERT: E 231 GLN cc_start: 0.9092 (pp30) cc_final: 0.8634 (pp30) REVERT: E 233 LEU cc_start: 0.9252 (tp) cc_final: 0.8694 (tp) REVERT: R 57 ARG cc_start: 0.9089 (tpp80) cc_final: 0.8809 (tpp80) REVERT: R 80 PHE cc_start: 0.8925 (m-10) cc_final: 0.8688 (m-10) REVERT: R 143 MET cc_start: 0.8764 (tpp) cc_final: 0.8434 (mpp) REVERT: R 214 MET cc_start: 0.8452 (tpp) cc_final: 0.8166 (tpt) REVERT: R 262 LEU cc_start: 0.8994 (tp) cc_final: 0.8703 (tp) REVERT: R 294 ASN cc_start: 0.8677 (t0) cc_final: 0.8243 (t0) outliers start: 26 outliers final: 20 residues processed: 236 average time/residue: 0.2341 time to fit residues: 71.8606 Evaluate side-chains 240 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 280 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 0.0020 chunk 18 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.072965 restraints weight = 17589.611| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.82 r_work: 0.2892 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8337 Z= 0.165 Angle : 0.553 9.909 11371 Z= 0.278 Chirality : 0.042 0.169 1349 Planarity : 0.004 0.047 1435 Dihedral : 6.714 116.449 1230 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.31 % Allowed : 18.80 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1110 helix: 1.67 (0.28), residues: 383 sheet: -0.66 (0.33), residues: 253 loop : -1.30 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 339 HIS 0.005 0.001 HIS B 183 PHE 0.018 0.001 PHE R 309 TYR 0.011 0.001 TYR E 235 ARG 0.011 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 0.880 Fit side-chains REVERT: A 8 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: A 20 ASP cc_start: 0.8290 (t0) cc_final: 0.7893 (t0) REVERT: A 255 ASN cc_start: 0.9023 (m-40) cc_final: 0.8337 (m-40) REVERT: A 274 PHE cc_start: 0.9024 (t80) cc_final: 0.8702 (t80) REVERT: A 350 ASP cc_start: 0.8923 (t0) cc_final: 0.8672 (t0) REVERT: B 217 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8525 (ptp) REVERT: B 228 ASP cc_start: 0.7666 (p0) cc_final: 0.7365 (p0) REVERT: B 261 LEU cc_start: 0.9143 (mp) cc_final: 0.8881 (mp) REVERT: B 292 PHE cc_start: 0.8858 (m-10) cc_final: 0.8602 (m-10) REVERT: B 297 TRP cc_start: 0.9001 (m100) cc_final: 0.8497 (m100) REVERT: E 52 SER cc_start: 0.8380 (t) cc_final: 0.7782 (p) REVERT: E 83 MET cc_start: 0.7887 (mmp) cc_final: 0.7522 (mmp) REVERT: E 93 MET cc_start: 0.7759 (tmm) cc_final: 0.7168 (tmm) REVERT: E 231 GLN cc_start: 0.9110 (pp30) cc_final: 0.8599 (pp30) REVERT: E 233 LEU cc_start: 0.9253 (tp) cc_final: 0.8636 (tp) REVERT: R 57 ARG cc_start: 0.9092 (tpp80) cc_final: 0.8825 (tpp80) REVERT: R 80 PHE cc_start: 0.8940 (m-10) cc_final: 0.8702 (m-10) REVERT: R 143 MET cc_start: 0.8780 (tpp) cc_final: 0.8490 (mpp) REVERT: R 214 MET cc_start: 0.8450 (tpp) cc_final: 0.8178 (tpt) REVERT: R 262 LEU cc_start: 0.9008 (tp) cc_final: 0.8739 (tp) REVERT: R 294 ASN cc_start: 0.8700 (t0) cc_final: 0.8293 (t0) outliers start: 33 outliers final: 24 residues processed: 236 average time/residue: 0.2324 time to fit residues: 71.5559 Evaluate side-chains 246 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 280 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 60 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.083707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.073005 restraints weight = 17667.962| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.83 r_work: 0.2892 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8337 Z= 0.168 Angle : 0.571 12.424 11371 Z= 0.284 Chirality : 0.042 0.165 1349 Planarity : 0.004 0.050 1435 Dihedral : 6.707 115.893 1230 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.79 % Allowed : 20.50 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1110 helix: 1.78 (0.28), residues: 383 sheet: -0.64 (0.33), residues: 256 loop : -1.26 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.005 0.001 HIS B 183 PHE 0.014 0.001 PHE B 222 TYR 0.011 0.001 TYR E 235 ARG 0.012 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 0.905 Fit side-chains REVERT: A 8 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: A 20 ASP cc_start: 0.8302 (t0) cc_final: 0.7905 (t0) REVERT: A 255 ASN cc_start: 0.9036 (m-40) cc_final: 0.8335 (m-40) REVERT: A 350 ASP cc_start: 0.8924 (t0) cc_final: 0.8692 (t0) REVERT: B 36 ASN cc_start: 0.8669 (p0) cc_final: 0.8434 (p0) REVERT: B 217 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8506 (ptp) REVERT: B 228 ASP cc_start: 0.7667 (p0) cc_final: 0.7348 (p0) REVERT: B 232 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8775 (tt) REVERT: B 261 LEU cc_start: 0.9143 (mp) cc_final: 0.8876 (mp) REVERT: B 292 PHE cc_start: 0.8905 (m-10) cc_final: 0.8611 (m-10) REVERT: B 297 TRP cc_start: 0.8996 (m100) cc_final: 0.8527 (m100) REVERT: E 52 SER cc_start: 0.8355 (t) cc_final: 0.7749 (p) REVERT: E 83 MET cc_start: 0.7830 (mmp) cc_final: 0.7503 (mmp) REVERT: E 93 MET cc_start: 0.7767 (tmm) cc_final: 0.7152 (tmm) REVERT: E 231 GLN cc_start: 0.9087 (pp30) cc_final: 0.8587 (pp30) REVERT: E 233 LEU cc_start: 0.9256 (tp) cc_final: 0.8613 (tp) REVERT: R 57 ARG cc_start: 0.9085 (tpp80) cc_final: 0.8818 (tpp80) REVERT: R 80 PHE cc_start: 0.8948 (m-10) cc_final: 0.8738 (m-10) REVERT: R 143 MET cc_start: 0.8792 (tpp) cc_final: 0.8490 (mpp) REVERT: R 214 MET cc_start: 0.8445 (tpp) cc_final: 0.8189 (tpt) REVERT: R 262 LEU cc_start: 0.9048 (tp) cc_final: 0.8743 (tp) REVERT: R 294 ASN cc_start: 0.8710 (t0) cc_final: 0.8300 (t0) REVERT: R 310 ARG cc_start: 0.8749 (mtm110) cc_final: 0.8521 (mtm110) outliers start: 29 outliers final: 21 residues processed: 234 average time/residue: 0.2219 time to fit residues: 68.4194 Evaluate side-chains 243 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 280 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.081001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.070197 restraints weight = 17797.132| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.82 r_work: 0.2837 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8337 Z= 0.303 Angle : 0.615 10.650 11371 Z= 0.315 Chirality : 0.044 0.176 1349 Planarity : 0.004 0.055 1435 Dihedral : 6.921 115.637 1230 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.79 % Allowed : 20.37 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1110 helix: 1.68 (0.27), residues: 384 sheet: -0.74 (0.32), residues: 265 loop : -1.17 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 267 HIS 0.009 0.001 HIS B 183 PHE 0.014 0.001 PHE B 222 TYR 0.019 0.001 TYR C 40 ARG 0.013 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 0.879 Fit side-chains REVERT: A 8 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8066 (pm20) REVERT: A 20 ASP cc_start: 0.8403 (t0) cc_final: 0.8004 (t0) REVERT: A 255 ASN cc_start: 0.9071 (m-40) cc_final: 0.8420 (m-40) REVERT: A 256 ASN cc_start: 0.9064 (t0) cc_final: 0.8722 (t0) REVERT: A 350 ASP cc_start: 0.8974 (t0) cc_final: 0.8706 (t0) REVERT: B 36 ASN cc_start: 0.8727 (p0) cc_final: 0.8401 (p0) REVERT: B 217 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8652 (ptp) REVERT: B 228 ASP cc_start: 0.7831 (p0) cc_final: 0.7531 (p0) REVERT: B 232 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8783 (tt) REVERT: B 243 THR cc_start: 0.9015 (t) cc_final: 0.8697 (p) REVERT: B 261 LEU cc_start: 0.9158 (mp) cc_final: 0.8886 (mp) REVERT: B 292 PHE cc_start: 0.9099 (m-10) cc_final: 0.8818 (m-10) REVERT: E 39 GLN cc_start: 0.8997 (tt0) cc_final: 0.8760 (tt0) REVERT: E 83 MET cc_start: 0.8025 (mmp) cc_final: 0.7632 (mmp) REVERT: E 233 LEU cc_start: 0.9330 (tp) cc_final: 0.9071 (tp) REVERT: R 57 ARG cc_start: 0.9051 (tpp80) cc_final: 0.8771 (tpp80) REVERT: R 80 PHE cc_start: 0.9003 (m-10) cc_final: 0.8773 (m-10) REVERT: R 214 MET cc_start: 0.8579 (tpp) cc_final: 0.8218 (tpt) REVERT: R 262 LEU cc_start: 0.9057 (tp) cc_final: 0.8712 (tp) REVERT: R 294 ASN cc_start: 0.8716 (t0) cc_final: 0.8278 (t0) outliers start: 29 outliers final: 24 residues processed: 226 average time/residue: 0.2216 time to fit residues: 65.8459 Evaluate side-chains 239 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 280 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 80 optimal weight: 0.8980 chunk 82 optimal weight: 0.0370 chunk 47 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 37 optimal weight: 0.0370 chunk 14 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.083779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.073043 restraints weight = 17842.315| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.86 r_work: 0.2892 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8337 Z= 0.148 Angle : 0.581 15.376 11371 Z= 0.288 Chirality : 0.042 0.171 1349 Planarity : 0.004 0.055 1435 Dihedral : 6.741 115.568 1230 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.87 % Allowed : 21.80 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1110 helix: 1.85 (0.28), residues: 383 sheet: -0.63 (0.32), residues: 265 loop : -1.22 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 36 HIS 0.004 0.001 HIS B 183 PHE 0.020 0.001 PHE R 309 TYR 0.017 0.001 TYR C 40 ARG 0.014 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.941 Fit side-chains REVERT: A 8 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8205 (pt0) REVERT: A 20 ASP cc_start: 0.8337 (t0) cc_final: 0.7954 (t0) REVERT: A 255 ASN cc_start: 0.9063 (m-40) cc_final: 0.8382 (m-40) REVERT: A 256 ASN cc_start: 0.9031 (t0) cc_final: 0.8677 (t0) REVERT: A 350 ASP cc_start: 0.8920 (t0) cc_final: 0.8684 (t0) REVERT: B 36 ASN cc_start: 0.8698 (p0) cc_final: 0.8388 (p0) REVERT: B 217 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8555 (ptp) REVERT: B 228 ASP cc_start: 0.7653 (p0) cc_final: 0.7329 (p0) REVERT: B 232 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8806 (tt) REVERT: B 243 THR cc_start: 0.8952 (t) cc_final: 0.8697 (p) REVERT: B 261 LEU cc_start: 0.9139 (mp) cc_final: 0.8866 (mp) REVERT: B 292 PHE cc_start: 0.9005 (m-10) cc_final: 0.8740 (m-10) REVERT: B 297 TRP cc_start: 0.8992 (m100) cc_final: 0.8495 (m100) REVERT: E 83 MET cc_start: 0.7866 (mmp) cc_final: 0.7563 (mmp) REVERT: E 93 MET cc_start: 0.7888 (tmm) cc_final: 0.7375 (tmm) REVERT: E 231 GLN cc_start: 0.9078 (pp30) cc_final: 0.8871 (pp30) REVERT: E 233 LEU cc_start: 0.9271 (tp) cc_final: 0.8968 (tp) REVERT: R 57 ARG cc_start: 0.9043 (tpp80) cc_final: 0.8772 (tpp80) REVERT: R 80 PHE cc_start: 0.8959 (m-10) cc_final: 0.8734 (m-10) REVERT: R 143 MET cc_start: 0.8805 (tpp) cc_final: 0.8519 (mmm) REVERT: R 214 MET cc_start: 0.8474 (tpp) cc_final: 0.8202 (tpt) REVERT: R 262 LEU cc_start: 0.9042 (tp) cc_final: 0.8838 (tp) REVERT: R 310 ARG cc_start: 0.8719 (mtm110) cc_final: 0.8350 (mtm110) outliers start: 22 outliers final: 18 residues processed: 226 average time/residue: 0.2271 time to fit residues: 67.9718 Evaluate side-chains 237 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 280 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN R 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.082889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.072174 restraints weight = 17587.254| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.82 r_work: 0.2875 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8337 Z= 0.203 Angle : 0.593 11.958 11371 Z= 0.297 Chirality : 0.043 0.162 1349 Planarity : 0.004 0.061 1435 Dihedral : 6.766 115.041 1230 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.13 % Allowed : 22.06 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 1110 helix: 1.82 (0.28), residues: 383 sheet: -0.55 (0.32), residues: 262 loop : -1.14 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.006 0.001 HIS B 183 PHE 0.011 0.001 PHE B 222 TYR 0.018 0.001 TYR C 40 ARG 0.015 0.001 ARG E 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.845 Fit side-chains REVERT: A 8 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8229 (pt0) REVERT: A 20 ASP cc_start: 0.8370 (t0) cc_final: 0.7993 (t0) REVERT: A 255 ASN cc_start: 0.9066 (m-40) cc_final: 0.8385 (m-40) REVERT: A 256 ASN cc_start: 0.9058 (t0) cc_final: 0.8710 (t0) REVERT: A 350 ASP cc_start: 0.8931 (t0) cc_final: 0.8696 (t0) REVERT: B 36 ASN cc_start: 0.8713 (p0) cc_final: 0.8410 (p0) REVERT: B 217 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8569 (ptp) REVERT: B 228 ASP cc_start: 0.7725 (p0) cc_final: 0.7461 (p0) REVERT: B 232 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8765 (tt) REVERT: B 243 THR cc_start: 0.8960 (t) cc_final: 0.8700 (p) REVERT: B 261 LEU cc_start: 0.9152 (mp) cc_final: 0.8876 (mp) REVERT: B 292 PHE cc_start: 0.9031 (m-10) cc_final: 0.8787 (m-10) REVERT: E 52 SER cc_start: 0.8472 (t) cc_final: 0.7870 (p) REVERT: E 69 THR cc_start: 0.8797 (t) cc_final: 0.8525 (m) REVERT: E 83 MET cc_start: 0.7886 (mmp) cc_final: 0.7599 (mmp) REVERT: E 231 GLN cc_start: 0.9106 (pp30) cc_final: 0.8891 (pp30) REVERT: E 233 LEU cc_start: 0.9302 (tp) cc_final: 0.8979 (tp) REVERT: R 57 ARG cc_start: 0.9045 (tpp80) cc_final: 0.8775 (tpp80) REVERT: R 143 MET cc_start: 0.8851 (tpp) cc_final: 0.8505 (mmm) REVERT: R 214 MET cc_start: 0.8525 (tpp) cc_final: 0.8210 (tpt) REVERT: R 262 LEU cc_start: 0.8996 (tp) cc_final: 0.8669 (tp) REVERT: R 294 ASN cc_start: 0.8647 (t0) cc_final: 0.8304 (t0) outliers start: 24 outliers final: 19 residues processed: 220 average time/residue: 0.2193 time to fit residues: 63.8758 Evaluate side-chains 232 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 280 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 22 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.083782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073040 restraints weight = 17832.616| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.87 r_work: 0.2892 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8337 Z= 0.169 Angle : 0.594 15.743 11371 Z= 0.292 Chirality : 0.042 0.165 1349 Planarity : 0.004 0.060 1435 Dihedral : 6.714 114.765 1230 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.74 % Allowed : 22.45 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1110 helix: 1.87 (0.28), residues: 383 sheet: -0.50 (0.32), residues: 262 loop : -1.13 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 36 HIS 0.005 0.001 HIS B 183 PHE 0.012 0.001 PHE B 222 TYR 0.018 0.001 TYR C 40 ARG 0.014 0.001 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3688.49 seconds wall clock time: 66 minutes 7.50 seconds (3967.50 seconds total)