Starting phenix.real_space_refine on Sun Dec 29 13:09:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y65_33634/12_2024/7y65_33634_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y65_33634/12_2024/7y65_33634.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/7y65_33634/12_2024/7y65_33634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y65_33634/12_2024/7y65_33634.map" model { file = "/net/cci-nas-00/data/ceres_data/7y65_33634/12_2024/7y65_33634_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y65_33634/12_2024/7y65_33634_neut.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= 0.001 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2112 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5584 2.51 5 N 1476 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8721 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 50 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'ZAL:plan-1': 1, 'ALC:plan-1': 1, 'MEA:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain: "S" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1515 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Chain breaks: 4 Chain: "D" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2246 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 13, 'TRANS': 269} Time building chain proxies: 5.78, per 1000 atoms: 0.66 Number of scatterers: 8721 At special positions: 0 Unit cell: (85.85, 115.6, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1601 8.00 N 1476 7.00 C 5584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 188 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.1 seconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAR L 6 " Input volumes are d-peptide like pdb=" CB ZAL L 4 " Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 38.1% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 removed outlier: 3.680A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.542A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.672A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.962A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.525A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.796A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.600A 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 'S' and resid 28 through 32 removed outlier: 3.643A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.919A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'D' and resid 34 through 65 removed outlier: 3.751A pdb=" N ILE D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU D 39 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 88 removed outlier: 3.986A pdb=" N ILE D 73 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU D 78 " --> pdb=" O TRP D 74 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 4.000A pdb=" N LEU D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 139 removed outlier: 4.242A pdb=" N ALA D 108 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Proline residue: D 113 - end of helix removed outlier: 4.237A pdb=" N ILE D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 removed outlier: 3.505A pdb=" N ASN D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 174 removed outlier: 3.854A pdb=" N ALA D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU D 165 " --> pdb=" O TRP D 161 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Proline residue: D 170 - end of helix Processing helix chain 'D' and resid 195 through 230 Proline residue: D 214 - end of helix Processing helix chain 'D' and resid 238 through 268 removed outlier: 3.712A pdb=" N LYS D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Proline residue: D 257 - end of helix removed outlier: 3.556A pdb=" N MET D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 303 removed outlier: 3.512A pdb=" N LEU D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N CYS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS D 294 " --> pdb=" O TYR D 290 " (cutoff:3.500A) Proline residue: D 297 - end of helix removed outlier: 3.959A pdb=" N TYR D 300 " --> pdb=" O ASN D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.473A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.544A 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 51 removed outlier: 5.908A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.808A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.757A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.128A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.777A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.647A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.676A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 5 removed outlier: 3.590A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 4.868A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 69 through 73 Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 6.703A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR S 243 " --> pdb=" O TYR S 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 175 through 180 removed outlier: 3.765A pdb=" N VAL D 176 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS D 185 " --> pdb=" O GLU D 180 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1116 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: 2.41 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2788 1.35 - 1.46: 2186 1.46 - 1.58: 3851 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 8909 Sorted by residual: bond pdb=" N HIS D 194 " pdb=" CA HIS D 194 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.08e-02 8.57e+03 6.14e+00 bond pdb=" N PHE D 211 " pdb=" CA PHE D 211 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.25e-02 6.40e+03 6.10e+00 bond pdb=" N LYS D 279 " pdb=" CA LYS D 279 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.78e+00 bond pdb=" N SER D 193 " pdb=" CA SER D 193 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.46e+00 bond pdb=" N ARG D 178 " pdb=" CA ARG D 178 " ideal model delta sigma weight residual 1.455 1.483 -0.027 1.23e-02 6.61e+03 4.99e+00 ... (remaining 8904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 11711 1.53 - 3.06: 290 3.06 - 4.59: 47 4.59 - 6.12: 14 6.12 - 7.65: 3 Bond angle restraints: 12065 Sorted by residual: angle pdb=" CA PRO D 297 " pdb=" N PRO D 297 " pdb=" CD PRO D 297 " ideal model delta sigma weight residual 112.00 105.51 6.49 1.40e+00 5.10e-01 2.15e+01 angle pdb=" CA VAL D 190 " pdb=" C VAL D 190 " pdb=" O VAL D 190 " ideal model delta sigma weight residual 121.97 118.23 3.74 9.80e-01 1.04e+00 1.46e+01 angle pdb=" C GLY D 210 " pdb=" N PHE D 211 " pdb=" CA PHE D 211 " ideal model delta sigma weight residual 122.79 116.90 5.89 1.70e+00 3.46e-01 1.20e+01 angle pdb=" C ARG D 206 " pdb=" CA ARG D 206 " pdb=" CB ARG D 206 " ideal model delta sigma weight residual 110.85 105.45 5.40 1.70e+00 3.46e-01 1.01e+01 angle pdb=" N ASP D 195 " pdb=" CA ASP D 195 " pdb=" C ASP D 195 " ideal model delta sigma weight residual 113.20 108.95 4.25 1.36e+00 5.41e-01 9.77e+00 ... (remaining 12060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.29: 4895 22.29 - 44.58: 329 44.58 - 66.86: 27 66.86 - 89.15: 7 89.15 - 111.44: 6 Dihedral angle restraints: 5264 sinusoidal: 2053 harmonic: 3211 Sorted by residual: dihedral pdb=" CA PRO D 183 " pdb=" C PRO D 183 " pdb=" N PRO D 184 " pdb=" CA PRO D 184 " ideal model delta harmonic sigma weight residual 180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CG ALC L 5 " pdb=" CD2 ALC L 5 " pdb=" CE2 ALC L 5 " pdb=" CZ ALC L 5 " ideal model delta sinusoidal sigma weight residual 55.58 -55.86 111.44 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" CD1 ALC L 5 " pdb=" CE1 ALC L 5 " pdb=" CZ ALC L 5 " pdb=" CE2 ALC L 5 " ideal model delta sinusoidal sigma weight residual 55.37 -55.44 110.81 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 5261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.032: 1369 1.032 - 2.064: 0 2.064 - 3.096: 0 3.096 - 4.128: 0 4.128 - 5.160: 1 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CG ALC L 5 " pdb=" CB ALC L 5 " pdb=" CD1 ALC L 5 " pdb=" CD2 ALC L 5 " both_signs ideal model delta sigma weight residual False -2.52 2.64 -5.16 2.00e-01 2.50e+01 6.66e+02 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CA PRO D 297 " pdb=" N PRO D 297 " pdb=" C PRO D 297 " pdb=" CB PRO D 297 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 1367 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 296 " 0.061 5.00e-02 4.00e+02 8.85e-02 1.25e+01 pdb=" N PRO D 297 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO D 297 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 297 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD DAR L 6 " -0.233 9.50e-02 1.11e+02 1.05e-01 6.71e+00 pdb=" NE DAR L 6 " 0.014 2.00e-02 2.50e+03 pdb=" CZ DAR L 6 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 DAR L 6 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 DAR L 6 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.043 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PRO B 39 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.035 5.00e-02 4.00e+02 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 396 2.73 - 3.27: 8385 3.27 - 3.81: 13860 3.81 - 4.36: 15930 4.36 - 4.90: 28735 Nonbonded interactions: 67306 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.183 3.040 nonbonded pdb=" O GLY D 51 " pdb=" ND2 ASN D 55 " model vdw 2.216 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.236 3.040 nonbonded pdb=" NE2 HIS S 35 " pdb=" OH TYR S 101 " model vdw 2.260 3.120 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.287 3.040 ... (remaining 67301 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.530 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 8909 Z= 0.181 Angle : 0.591 7.651 12065 Z= 0.342 Chirality : 0.146 5.160 1370 Planarity : 0.005 0.105 1515 Dihedral : 14.435 111.440 3182 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.68 % Rotamer: Outliers : 0.85 % Allowed : 0.32 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.35 (0.26), residues: 1084 helix: 1.89 (0.27), residues: 358 sheet: 0.49 (0.34), residues: 242 loop : -1.21 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 255 HIS 0.003 0.001 HIS A 188 PHE 0.034 0.001 PHE D 44 TYR 0.008 0.001 TYR S 101 ARG 0.012 0.001 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.990 Fit side-chains REVERT: A 304 GLN cc_start: 0.6967 (tm-30) cc_final: 0.6673 (tm-30) REVERT: A 309 ASP cc_start: 0.6235 (m-30) cc_final: 0.5984 (m-30) REVERT: B 262 MET cc_start: 0.7306 (tpp) cc_final: 0.6989 (mmm) outliers start: 8 outliers final: 3 residues processed: 133 average time/residue: 0.2203 time to fit residues: 41.8937 Evaluate side-chains 93 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 194 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0070 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 overall best weight: 1.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8909 Z= 0.273 Angle : 0.631 8.135 12065 Z= 0.332 Chirality : 0.045 0.243 1370 Planarity : 0.005 0.055 1515 Dihedral : 6.431 89.961 1216 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.27 % Allowed : 7.74 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.31 (0.25), residues: 1084 helix: 1.96 (0.27), residues: 367 sheet: 0.22 (0.33), residues: 258 loop : -1.29 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 332 HIS 0.010 0.002 HIS B 54 PHE 0.018 0.002 PHE A 196 TYR 0.021 0.002 TYR B 105 ARG 0.005 0.001 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 1.099 Fit side-chains REVERT: A 309 ASP cc_start: 0.6414 (m-30) cc_final: 0.6193 (m-30) REVERT: D 193 SER cc_start: 0.7185 (OUTLIER) cc_final: 0.6982 (p) outliers start: 12 outliers final: 7 residues processed: 114 average time/residue: 0.2115 time to fit residues: 34.2976 Evaluate side-chains 104 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 193 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 268 ASN D 119 ASN D 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8909 Z= 0.176 Angle : 0.546 8.494 12065 Z= 0.286 Chirality : 0.042 0.247 1370 Planarity : 0.004 0.047 1515 Dihedral : 5.841 78.442 1214 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.59 % Allowed : 10.60 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.45 (0.26), residues: 1084 helix: 2.10 (0.27), residues: 366 sheet: 0.34 (0.32), residues: 264 loop : -1.27 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 332 HIS 0.004 0.001 HIS B 54 PHE 0.011 0.001 PHE D 75 TYR 0.013 0.001 TYR D 174 ARG 0.003 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 47 TRP cc_start: 0.5981 (t60) cc_final: 0.5446 (t60) REVERT: D 280 LYS cc_start: 0.8188 (mmtp) cc_final: 0.7928 (mmtm) REVERT: D 290 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.6957 (m-80) outliers start: 15 outliers final: 9 residues processed: 113 average time/residue: 0.2317 time to fit residues: 36.2913 Evaluate side-chains 104 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 290 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 255 ASN B 75 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8909 Z= 0.300 Angle : 0.643 7.369 12065 Z= 0.337 Chirality : 0.046 0.295 1370 Planarity : 0.005 0.046 1515 Dihedral : 6.100 80.254 1214 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.55 % Allowed : 13.26 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.26 (0.26), residues: 1084 helix: 1.87 (0.27), residues: 367 sheet: 0.22 (0.32), residues: 272 loop : -1.34 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 332 HIS 0.005 0.001 HIS B 54 PHE 0.022 0.002 PHE S 239 TYR 0.018 0.002 TYR S 60 ARG 0.004 0.001 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 276 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: B 262 MET cc_start: 0.7561 (tpp) cc_final: 0.7265 (mtt) REVERT: B 284 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8120 (mp) REVERT: B 338 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7787 (mp) REVERT: S 47 TRP cc_start: 0.6250 (t60) cc_final: 0.5917 (t60) REVERT: D 280 LYS cc_start: 0.8329 (mmtp) cc_final: 0.8127 (mmtm) outliers start: 24 outliers final: 16 residues processed: 121 average time/residue: 0.2163 time to fit residues: 36.5656 Evaluate side-chains 114 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 267 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 0.0000 chunk 35 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 255 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8909 Z= 0.159 Angle : 0.542 7.926 12065 Z= 0.284 Chirality : 0.042 0.284 1370 Planarity : 0.004 0.048 1515 Dihedral : 5.722 75.514 1214 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.33 % Allowed : 15.59 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.44 (0.26), residues: 1084 helix: 2.12 (0.28), residues: 366 sheet: 0.22 (0.31), residues: 281 loop : -1.27 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 332 HIS 0.003 0.001 HIS A 188 PHE 0.010 0.001 PHE D 75 TYR 0.015 0.001 TYR D 174 ARG 0.003 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 276 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: B 105 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.7017 (t80) REVERT: B 215 GLU cc_start: 0.6690 (mp0) cc_final: 0.6384 (mp0) REVERT: B 234 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7454 (t80) REVERT: B 262 MET cc_start: 0.7651 (tpp) cc_final: 0.7368 (mtt) REVERT: B 332 TRP cc_start: 0.6921 (m100) cc_final: 0.6628 (m-10) REVERT: B 338 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7789 (mt) REVERT: D 290 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7130 (m-80) outliers start: 22 outliers final: 12 residues processed: 113 average time/residue: 0.2005 time to fit residues: 31.8095 Evaluate side-chains 108 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 290 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8909 Z= 0.206 Angle : 0.583 14.760 12065 Z= 0.300 Chirality : 0.043 0.310 1370 Planarity : 0.004 0.048 1515 Dihedral : 5.735 76.888 1214 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.86 % Allowed : 15.16 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.37 (0.26), residues: 1084 helix: 1.98 (0.28), residues: 366 sheet: 0.16 (0.31), residues: 284 loop : -1.22 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 332 HIS 0.004 0.001 HIS A 213 PHE 0.013 0.002 PHE A 196 TYR 0.016 0.002 TYR D 174 ARG 0.003 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7459 (ttp-170) cc_final: 0.7138 (ttm170) REVERT: A 23 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.5707 (mp) REVERT: A 276 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: B 105 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7253 (t80) REVERT: B 262 MET cc_start: 0.7644 (tpp) cc_final: 0.7406 (mtt) REVERT: B 338 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7764 (mt) REVERT: S 109 ASP cc_start: 0.6063 (OUTLIER) cc_final: 0.5755 (m-30) REVERT: D 104 PHE cc_start: 0.5440 (t80) cc_final: 0.5105 (t80) REVERT: D 290 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7178 (m-80) outliers start: 27 outliers final: 14 residues processed: 118 average time/residue: 0.2401 time to fit residues: 39.2646 Evaluate side-chains 113 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain D residue 295 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.3980 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 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 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8909 Z= 0.157 Angle : 0.560 12.915 12065 Z= 0.285 Chirality : 0.042 0.307 1370 Planarity : 0.003 0.049 1515 Dihedral : 5.551 74.811 1214 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.23 % Allowed : 17.07 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.49 (0.26), residues: 1084 helix: 2.11 (0.28), residues: 367 sheet: 0.32 (0.31), residues: 280 loop : -1.25 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP S 47 HIS 0.004 0.001 HIS A 188 PHE 0.012 0.001 PHE S 177 TYR 0.017 0.001 TYR D 174 ARG 0.002 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.5641 (mp) REVERT: A 276 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: B 105 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.6940 (t80) REVERT: B 234 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7527 (t80) REVERT: B 262 MET cc_start: 0.7647 (tpp) cc_final: 0.7390 (mtt) REVERT: B 332 TRP cc_start: 0.7079 (m100) cc_final: 0.6682 (m-10) REVERT: B 338 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7743 (mt) REVERT: D 290 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7163 (m-80) outliers start: 21 outliers final: 13 residues processed: 112 average time/residue: 0.2158 time to fit residues: 33.7772 Evaluate side-chains 113 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain D residue 295 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8909 Z= 0.274 Angle : 0.625 11.507 12065 Z= 0.322 Chirality : 0.044 0.311 1370 Planarity : 0.004 0.048 1515 Dihedral : 5.680 76.818 1212 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.76 % Allowed : 16.54 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.29 (0.26), residues: 1084 helix: 1.88 (0.28), residues: 369 sheet: 0.17 (0.32), residues: 277 loop : -1.27 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 332 HIS 0.005 0.001 HIS A 213 PHE 0.014 0.002 PHE S 29 TYR 0.018 0.002 TYR D 174 ARG 0.004 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7483 (ttp-170) cc_final: 0.7162 (ttm170) REVERT: A 23 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.5715 (mp) REVERT: A 276 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: B 105 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.7413 (t80) REVERT: B 234 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7487 (t80) REVERT: B 332 TRP cc_start: 0.7357 (m100) cc_final: 0.6933 (m-10) REVERT: B 338 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7761 (mp) REVERT: S 109 ASP cc_start: 0.6116 (OUTLIER) cc_final: 0.5765 (m-30) REVERT: D 104 PHE cc_start: 0.5422 (t80) cc_final: 0.5132 (t80) REVERT: D 290 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.7303 (m-80) outliers start: 26 outliers final: 15 residues processed: 117 average time/residue: 0.2099 time to fit residues: 34.1241 Evaluate side-chains 117 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain D residue 295 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 0.0980 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 0.0170 chunk 63 optimal weight: 1.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8909 Z= 0.197 Angle : 0.590 11.024 12065 Z= 0.303 Chirality : 0.043 0.358 1370 Planarity : 0.004 0.049 1515 Dihedral : 5.606 75.542 1212 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.33 % Allowed : 17.07 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.34 (0.26), residues: 1084 helix: 1.93 (0.28), residues: 367 sheet: 0.22 (0.32), residues: 273 loop : -1.25 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 332 HIS 0.004 0.001 HIS A 213 PHE 0.011 0.001 PHE S 177 TYR 0.019 0.001 TYR D 174 ARG 0.004 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7476 (ttp-170) cc_final: 0.7155 (ttm170) REVERT: A 23 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.5659 (mp) REVERT: A 276 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: B 105 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.7206 (t80) REVERT: B 234 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7473 (t80) REVERT: B 338 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7786 (mt) REVERT: S 109 ASP cc_start: 0.6084 (OUTLIER) cc_final: 0.5793 (m-30) REVERT: D 104 PHE cc_start: 0.5422 (t80) cc_final: 0.5133 (t80) REVERT: D 290 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7248 (m-80) outliers start: 22 outliers final: 14 residues processed: 111 average time/residue: 0.2216 time to fit residues: 34.1533 Evaluate side-chains 114 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 290 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8909 Z= 0.166 Angle : 0.567 10.677 12065 Z= 0.291 Chirality : 0.042 0.339 1370 Planarity : 0.003 0.049 1515 Dihedral : 5.427 75.124 1212 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.12 % Allowed : 17.60 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.43 (0.26), residues: 1084 helix: 1.98 (0.28), residues: 368 sheet: 0.32 (0.32), residues: 275 loop : -1.23 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 332 HIS 0.005 0.001 HIS A 188 PHE 0.013 0.001 PHE S 177 TYR 0.016 0.001 TYR D 174 ARG 0.002 0.000 ARG S 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7454 (ttp-170) cc_final: 0.7136 (ttm170) REVERT: A 23 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.5627 (mp) REVERT: A 276 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: B 105 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.6913 (t80) REVERT: B 234 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7570 (t80) REVERT: B 338 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7761 (mt) REVERT: S 109 ASP cc_start: 0.6052 (OUTLIER) cc_final: 0.5842 (m-30) REVERT: S 140 MET cc_start: 0.4249 (mmp) cc_final: 0.4041 (mmp) REVERT: D 104 PHE cc_start: 0.5364 (t80) cc_final: 0.5085 (t80) REVERT: D 290 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7238 (m-80) outliers start: 20 outliers final: 13 residues processed: 106 average time/residue: 0.2096 time to fit residues: 31.3606 Evaluate side-chains 109 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 290 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.179045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141084 restraints weight = 11192.612| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.32 r_work: 0.3579 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 8909 Z= 0.307 Angle : 0.662 10.237 12065 Z= 0.342 Chirality : 0.046 0.360 1370 Planarity : 0.004 0.048 1515 Dihedral : 5.739 77.388 1212 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.44 % Allowed : 17.39 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1084 helix: 1.68 (0.28), residues: 372 sheet: 0.14 (0.32), residues: 274 loop : -1.27 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 332 HIS 0.006 0.001 HIS A 213 PHE 0.019 0.002 PHE S 32 TYR 0.019 0.002 TYR B 59 ARG 0.004 0.000 ARG S 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1982.74 seconds wall clock time: 37 minutes 36.42 seconds (2256.42 seconds total)