Starting phenix.real_space_refine on Sat Jul 4 18:29:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nhq_12337/07_2026/7nhq_12337.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nhq_12337/07_2026/7nhq_12337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7nhq_12337/07_2026/7nhq_12337.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nhq_12337/07_2026/7nhq_12337.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nhq_12337/07_2026/7nhq_12337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nhq_12337/07_2026/7nhq_12337.map" model { file = "/net/cci-nas-00/data/ceres_data/7nhq_12337/07_2026/7nhq_12337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nhq_12337/07_2026/7nhq_12337.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 9 Type Number sf(0) Gaussians Mn 1 7.51 5 Fe 2 7.16 5 P 1 5.49 5 Mg 35 5.21 5 S 71 5.16 5 Cl 1 4.86 5 C 14488 2.51 5 N 3039 2.21 5 O 3308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20946 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2627 Classifications: {'peptide': 335} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 319} Chain: "B" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3909 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 32, 'TRANS': 463} Chain: "C" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3345 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain: "D" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2717 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 323} Chain: "E" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 635 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain: "F" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "H" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 511 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "I" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "K" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 293 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "L" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 304 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "M" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 267 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "T" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 241 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain: "X" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 254 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "y" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 208 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "Z" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 463 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "2" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 897 Classifications: {'peptide': 112} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 106} Chain: "3" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 419 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "A" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 286 Unusual residues: {' CL': 1, ' FE': 1, ' MN': 1, 'BCR': 1, 'CLA': 2, 'LHG': 1, 'PHO': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 1160 Unusual residues: {'BCR': 3, 'CLA': 16} Classifications: {'undetermined': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 1075 Unusual residues: {'BCR': 3, 'CLA': 13, 'LMG': 2} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 489 Unusual residues: {'CLA': 4, 'LMG': 2, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'BCR': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.17, per 1000 atoms: 0.15 Number of scatterers: 20946 At special positions: 0 Unit cell: (132.98, 109, 141.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Fe 2 26.01 Mn 1 24.99 Cl 1 17.00 S 71 16.00 P 1 15.00 Mg 35 11.99 O 3308 8.00 N 3039 7.00 C 14488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=19, symmetry=0 Number of additional bonds: simple=19, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 521.2 milliseconds 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4034 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 13 sheets defined 60.5% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.778A pdb=" N ARG A 16 " --> pdb=" O ASN A 12 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 22 " --> pdb=" O CYS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 55 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 108 removed outlier: 3.502A pdb=" N TRP A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 137 removed outlier: 4.018A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 removed outlier: 3.900A pdb=" N ALA A 146 " --> pdb=" O TRP A 142 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.753A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 222 removed outlier: 3.570A pdb=" N GLN A 199 " --> pdb=" O HIS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 255 removed outlier: 3.681A pdb=" N HIS A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 264 Processing helix chain 'A' and resid 268 through 294 removed outlier: 4.359A pdb=" N HIS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 318 through 332 removed outlier: 3.664A pdb=" N MET A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 44 Processing helix chain 'B' and resid 62 through 69 removed outlier: 4.134A pdb=" N LEU B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 194 through 219 removed outlier: 3.987A pdb=" N VAL B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 233 through 259 removed outlier: 4.060A pdb=" N VAL B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.874A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 277 " --> pdb=" O TYR B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 296 removed outlier: 3.638A pdb=" N GLN B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 306 through 313 removed outlier: 3.547A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.720A pdb=" N ASP B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 425 removed outlier: 3.821A pdb=" N VAL B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 475 removed outlier: 3.646A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'C' and resid 22 through 31 removed outlier: 3.509A pdb=" N ALA C 25 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 26 " --> pdb=" O TRP C 23 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN C 27 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 30 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE C 31 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 61 removed outlier: 3.651A pdb=" N LEU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 76 through 83 removed outlier: 3.680A pdb=" N LEU C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 123 removed outlier: 3.953A pdb=" N ALA C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 169 removed outlier: 3.719A pdb=" N MET C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 155 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 217 through 241 removed outlier: 3.552A pdb=" N VAL C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 257 through 281 removed outlier: 3.762A pdb=" N MET C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 313 removed outlier: 3.746A pdb=" N SER C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 346 Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 373 through 385 removed outlier: 4.353A pdb=" N THR C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 444 removed outlier: 3.552A pdb=" N TRP C 413 " --> pdb=" O SER C 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 23 removed outlier: 3.520A pdb=" N LYS D 23 " --> pdb=" O ASP D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 55 removed outlier: 3.695A pdb=" N ILE D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 108 through 137 removed outlier: 4.372A pdb=" N THR D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 146 removed outlier: 3.685A pdb=" N ILE D 144 " --> pdb=" O PRO D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 removed outlier: 3.588A pdb=" N ILE D 150 " --> pdb=" O PHE D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 164 removed outlier: 3.684A pdb=" N LEU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.761A pdb=" N PHE D 169 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 190 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 194 through 220 Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 245 through 257 removed outlier: 3.681A pdb=" N ALA D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 290 removed outlier: 3.666A pdb=" N LEU D 272 " --> pdb=" O HIS D 268 " (cutoff:3.500A) Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 313 through 334 Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 348 through 352 Processing helix chain 'E' and resid 16 through 40 removed outlier: 3.784A pdb=" N TRP E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ILE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Proline residue: E 28 - end of helix removed outlier: 4.066A pdb=" N VAL E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.710A pdb=" N GLN E 82 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 25 Processing helix chain 'F' and resid 27 through 40 removed outlier: 3.530A pdb=" N ALA F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 43 No H-bonds generated for 'chain 'F' and resid 41 through 43' Processing helix chain 'H' and resid 7 through 12 Processing helix chain 'H' and resid 13 through 16 removed outlier: 3.916A pdb=" N SER H 16 " --> pdb=" O PRO H 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 13 through 16' Processing helix chain 'H' and resid 27 through 50 removed outlier: 3.701A pdb=" N MET H 31 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 24 removed outlier: 3.524A pdb=" N PHE I 15 " --> pdb=" O VAL I 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 23 removed outlier: 4.281A pdb=" N ASP K 23 " --> pdb=" O ASP K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 43 removed outlier: 3.621A pdb=" N LEU K 31 " --> pdb=" O VAL K 27 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA K 34 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN K 40 " --> pdb=" O ALA K 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 36 removed outlier: 4.527A pdb=" N SER L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR L 34 " --> pdb=" O LEU L 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 31 removed outlier: 3.572A pdb=" N LEU M 8 " --> pdb=" O ASN M 4 " (cutoff:3.500A) Proline residue: M 18 - end of helix removed outlier: 3.894A pdb=" N SER M 31 " --> pdb=" O VAL M 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 23 Processing helix chain 'X' and resid 4 through 35 Processing helix chain 'y' and resid 22 through 42 removed outlier: 3.654A pdb=" N GLY y 29 " --> pdb=" O ILE y 25 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY y 32 " --> pdb=" O ILE y 28 " (cutoff:3.500A) Proline residue: y 33 - end of helix removed outlier: 3.918A pdb=" N ILE y 36 " --> pdb=" O GLY y 32 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU y 39 " --> pdb=" O ILE y 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA y 40 " --> pdb=" O ILE y 36 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL y 41 " --> pdb=" O PHE y 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 29 removed outlier: 3.602A pdb=" N ILE Z 21 " --> pdb=" O PHE Z 17 " (cutoff:3.500A) Proline residue: Z 24 - end of helix removed outlier: 3.511A pdb=" N SER Z 29 " --> pdb=" O VAL Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 32 through 58 removed outlier: 3.596A pdb=" N SER Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU Z 52 " --> pdb=" O ILE Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 59 through 61 No H-bonds generated for 'chain 'Z' and resid 59 through 61' Processing helix chain '2' and resid 88 through 106 Processing helix chain '3' and resid 27 through 55 removed outlier: 3.575A pdb=" N LEU 3 37 " --> pdb=" O ARG 3 33 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 227 removed outlier: 6.808A pdb=" N LEU A 223 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU A 244 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG A 225 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 241 " --> pdb=" O PHE 2 72 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA 2 79 " --> pdb=" O LYS 2 71 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE 2 73 " --> pdb=" O PRO 2 77 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER 2 31 " --> pdb=" O ALA 2 26 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP 2 20 " --> pdb=" O TYR 2 37 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU 2 23 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLU B 492 " --> pdb=" O LEU 2 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG 2 25 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 307 removed outlier: 4.408A pdb=" N VAL A 306 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AA6, first strand: chain 'B' and resid 336 through 340 removed outlier: 7.029A pdb=" N GLU B 431 " --> pdb=" O GLN B 338 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 377 through 380 removed outlier: 4.022A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AA9, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AB1, first strand: chain 'C' and resid 358 through 359 removed outlier: 3.712A pdb=" N GLY C 362 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AB4, first strand: chain '2' and resid 13 through 14 removed outlier: 4.476A pdb=" N ILE 2 10 " --> pdb=" O ILE 2 13 " (cutoff:3.500A) 970 hydrogen bonds defined for protein. 2796 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: 3.00 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.36: 6111 1.36 - 1.55: 15085 1.55 - 1.74: 327 1.74 - 1.93: 128 1.93 - 2.12: 144 Bond restraints: 21795 Sorted by residual: bond pdb=" C5 BCR H 101 " pdb=" C6 BCR H 101 " ideal model delta sigma weight residual 1.347 1.173 0.174 2.00e-02 2.50e+03 7.58e+01 bond pdb=" C3D CLA C 510 " pdb=" CAD CLA C 510 " ideal model delta sigma weight residual 1.454 1.605 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" C5 BCR K 101 " pdb=" C6 BCR K 101 " ideal model delta sigma weight residual 1.347 1.196 0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C3D CLA C 507 " pdb=" CAD CLA C 507 " ideal model delta sigma weight residual 1.454 1.590 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C1 BCR H 101 " pdb=" C6 BCR H 101 " ideal model delta sigma weight residual 1.532 1.397 0.135 2.00e-02 2.50e+03 4.53e+01 ... (remaining 21790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.48: 29051 5.48 - 10.96: 794 10.96 - 16.45: 211 16.45 - 21.93: 24 21.93 - 27.41: 9 Bond angle restraints: 30089 Sorted by residual: angle pdb=" CA GLU 3 7 " pdb=" CB GLU 3 7 " pdb=" CG GLU 3 7 " ideal model delta sigma weight residual 114.10 133.98 -19.88 2.00e+00 2.50e-01 9.88e+01 angle pdb=" CB GLU 3 7 " pdb=" CG GLU 3 7 " pdb=" CD GLU 3 7 " ideal model delta sigma weight residual 112.60 128.97 -16.37 1.70e+00 3.46e-01 9.27e+01 angle pdb=" C3A CLA C 513 " pdb=" C2A CLA C 513 " pdb=" CAA CLA C 513 " ideal model delta sigma weight residual 112.02 139.43 -27.41 3.00e+00 1.11e-01 8.35e+01 angle pdb=" C3A CLA B 616 " pdb=" C2A CLA B 616 " pdb=" CAA CLA B 616 " ideal model delta sigma weight residual 112.02 137.34 -25.32 3.00e+00 1.11e-01 7.12e+01 angle pdb=" C2A CLA B 604 " pdb=" C3A CLA B 604 " pdb=" CMA CLA B 604 " ideal model delta sigma weight residual 112.13 137.22 -25.09 3.00e+00 1.11e-01 6.99e+01 ... (remaining 30084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.07: 10456 26.07 - 52.14: 643 52.14 - 78.21: 138 78.21 - 104.28: 69 104.28 - 130.35: 12 Dihedral angle restraints: 11318 sinusoidal: 4995 harmonic: 6323 Sorted by residual: dihedral pdb=" CA ASN y 45 " pdb=" C ASN y 45 " pdb=" N LEU y 46 " pdb=" CA LEU y 46 " ideal model delta harmonic sigma weight residual 180.00 136.30 43.70 0 5.00e+00 4.00e-02 7.64e+01 dihedral pdb=" CA ARG 2 27 " pdb=" C ARG 2 27 " pdb=" N ASP 2 28 " pdb=" CA ASP 2 28 " ideal model delta harmonic sigma weight residual 180.00 -139.62 -40.38 0 5.00e+00 4.00e-02 6.52e+01 dihedral pdb=" CA ARG D 233 " pdb=" C ARG D 233 " pdb=" N ALA D 234 " pdb=" CA ALA D 234 " ideal model delta harmonic sigma weight residual 0.00 40.32 -40.32 0 5.00e+00 4.00e-02 6.50e+01 ... (remaining 11315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.884: 2836 0.884 - 1.768: 19 1.768 - 2.652: 28 2.652 - 3.536: 25 3.536 - 4.420: 6 Chirality restraints: 2914 Sorted by residual: chirality pdb=" C2A CLA B 601 " pdb=" C1A CLA B 601 " pdb=" C3A CLA B 601 " pdb=" CAA CLA B 601 " both_signs ideal model delta sigma weight residual False 2.84 -1.58 4.42 2.00e-01 2.50e+01 4.89e+02 chirality pdb=" C2A CLA B 609 " pdb=" C1A CLA B 609 " pdb=" C3A CLA B 609 " pdb=" CAA CLA B 609 " both_signs ideal model delta sigma weight residual False 2.84 -1.53 4.37 2.00e-01 2.50e+01 4.78e+02 chirality pdb=" C2A CLA B 614 " pdb=" C1A CLA B 614 " pdb=" C3A CLA B 614 " pdb=" CAA CLA B 614 " both_signs ideal model delta sigma weight residual False 2.84 -1.44 4.28 2.00e-01 2.50e+01 4.57e+02 ... (remaining 2911 not shown) Planarity restraints: 3788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 BCR K 101 " 0.087 2.00e-02 2.50e+03 1.59e-01 3.15e+02 pdb=" C21 BCR K 101 " -0.218 2.00e-02 2.50e+03 pdb=" C22 BCR K 101 " 0.248 2.00e-02 2.50e+03 pdb=" C23 BCR K 101 " -0.023 2.00e-02 2.50e+03 pdb=" C37 BCR K 101 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 BCR H 101 " -0.084 2.00e-02 2.50e+03 1.56e-01 3.04e+02 pdb=" C21 BCR H 101 " 0.213 2.00e-02 2.50e+03 pdb=" C22 BCR H 101 " -0.245 2.00e-02 2.50e+03 pdb=" C23 BCR H 101 " 0.024 2.00e-02 2.50e+03 pdb=" C37 BCR H 101 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 BCR C 518 " 0.112 2.00e-02 2.50e+03 1.15e-01 1.32e+02 pdb=" C7 BCR C 518 " -0.102 2.00e-02 2.50e+03 pdb=" C8 BCR C 518 " -0.127 2.00e-02 2.50e+03 pdb=" C9 BCR C 518 " 0.118 2.00e-02 2.50e+03 ... (remaining 3785 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 10 2.41 - 3.03: 11073 3.03 - 3.66: 29877 3.66 - 4.28: 47779 4.28 - 4.90: 78250 Nonbonded interactions: 166989 Sorted by model distance: nonbonded pdb=" NE2 HIS A 215 " pdb="FE FE A 401 " model vdw 1.790 2.340 nonbonded pdb=" NE2 HIS D 214 " pdb="FE FE A 401 " model vdw 1.950 2.340 nonbonded pdb=" NE2 HIS A 272 " pdb="FE FE A 401 " model vdw 2.216 2.340 nonbonded pdb=" O TYR C 200 " pdb=" O TRP C 211 " model vdw 2.358 3.040 nonbonded pdb=" O THR 2 85 " pdb=" NH1 ARG 2 87 " model vdw 2.360 3.120 ... (remaining 166984 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.650 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.021 0.725 21814 Z= 1.714 Angle : 2.313 27.411 30089 Z= 0.977 Chirality : 0.414 4.420 2914 Planarity : 0.017 0.159 3788 Dihedral : 19.449 130.346 7284 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.13 % Favored : 94.55 % Rotamer: Outliers : 1.77 % Allowed : 9.77 % Favored : 88.47 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.15), residues: 2203 helix: -1.31 (0.13), residues: 1219 sheet: -0.64 (0.58), residues: 77 loop : -2.26 (0.17), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.001 ARG E 8 TYR 0.055 0.004 TYR 3 3 PHE 0.133 0.006 PHE E 10 TRP 0.076 0.005 TRP 2 92 HIS 0.058 0.004 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.01236 / 0.61 (21795) covalent geometry : angle 2.31261 / 0.98 (30089) hydrogen bonds : bond 0.16815 / 10.95 ( 970) hydrogen bonds : angle 6.48755 / 4.68 ( 2796) Misc. bond : bond 0.57229 / 37.32 ( 19) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 784 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.9211 (t0) cc_final: 0.8914 (t0) REVERT: A 194 MET cc_start: 0.9088 (mmt) cc_final: 0.8834 (mmm) REVERT: A 225 ARG cc_start: 0.8506 (ptp90) cc_final: 0.8222 (ptp-110) REVERT: A 242 GLU cc_start: 0.7723 (mp0) cc_final: 0.6931 (mp0) REVERT: A 246 TYR cc_start: 0.6788 (p90) cc_final: 0.6522 (p90) REVERT: A 307 ILE cc_start: 0.9074 (pt) cc_final: 0.8868 (pp) REVERT: B 46 ASP cc_start: 0.8611 (t0) cc_final: 0.8020 (t0) REVERT: B 87 ASP cc_start: 0.7994 (t0) cc_final: 0.7769 (t70) REVERT: B 130 GLU cc_start: 0.8194 (mp0) cc_final: 0.7986 (mp0) REVERT: B 313 ASP cc_start: 0.9094 (t0) cc_final: 0.8727 (t0) REVERT: B 372 ASP cc_start: 0.8397 (p0) cc_final: 0.8046 (p0) REVERT: B 374 ASN cc_start: 0.8596 (m-40) cc_final: 0.8354 (p0) REVERT: B 380 ASP cc_start: 0.8804 (p0) cc_final: 0.8382 (p0) REVERT: B 477 ASP cc_start: 0.8868 (p0) cc_final: 0.8625 (p0) REVERT: C 154 ILE cc_start: 0.9221 (mt) cc_final: 0.8996 (mm) REVERT: C 183 ASP cc_start: 0.7805 (t70) cc_final: 0.7591 (t0) REVERT: C 193 ASP cc_start: 0.8314 (t0) cc_final: 0.8025 (t0) REVERT: C 282 ASN cc_start: 0.9324 (p0) cc_final: 0.9100 (p0) REVERT: C 350 ARG cc_start: 0.4798 (pmt170) cc_final: 0.3245 (mpt90) REVERT: D 16 ASP cc_start: 0.8666 (m-30) cc_final: 0.8408 (m-30) REVERT: D 19 ASP cc_start: 0.8836 (t0) cc_final: 0.8464 (t0) REVERT: D 20 ASP cc_start: 0.8524 (p0) cc_final: 0.8093 (p0) REVERT: D 68 LEU cc_start: 0.9474 (tp) cc_final: 0.9215 (tp) REVERT: D 69 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8644 (mt-10) REVERT: D 100 ASP cc_start: 0.8484 (t0) cc_final: 0.8184 (t0) REVERT: D 105 CYS cc_start: 0.9110 (m) cc_final: 0.8775 (m) REVERT: D 210 LEU cc_start: 0.8858 (mt) cc_final: 0.8606 (mt) REVERT: D 246 MET cc_start: 0.8806 (tpt) cc_final: 0.8508 (tpt) REVERT: D 263 ASN cc_start: 0.8837 (t0) cc_final: 0.8611 (t0) REVERT: D 307 GLU cc_start: 0.7696 (pp20) cc_final: 0.7493 (pp20) REVERT: E 62 SER cc_start: 0.8948 (m) cc_final: 0.8692 (p) REVERT: H 50 ASN cc_start: 0.9086 (t0) cc_final: 0.8882 (t0) REVERT: L 8 GLN cc_start: 0.8412 (mm110) cc_final: 0.8088 (mm-40) REVERT: L 11 GLU cc_start: 0.7784 (pt0) cc_final: 0.7068 (pt0) REVERT: M 5 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7015 (pm20) REVERT: X 8 LYS cc_start: 0.8430 (mtpp) cc_final: 0.7815 (tptt) REVERT: X 12 ILE cc_start: 0.9185 (mt) cc_final: 0.8960 (mp) REVERT: X 31 ILE cc_start: 0.9123 (tt) cc_final: 0.8839 (tt) REVERT: X 35 ASP cc_start: 0.7615 (p0) cc_final: 0.7337 (p0) REVERT: Z 6 GLN cc_start: 0.8529 (mt0) cc_final: 0.8171 (mt0) REVERT: 2 23 LEU cc_start: 0.8448 (tt) cc_final: 0.8050 (mt) REVERT: 2 35 MET cc_start: 0.7846 (mpp) cc_final: 0.7574 (mpp) REVERT: 2 42 LYS cc_start: 0.9028 (tptt) cc_final: 0.8752 (mmmt) REVERT: 2 46 GLU cc_start: 0.7992 (tp30) cc_final: 0.7702 (tp30) REVERT: 2 93 ASP cc_start: 0.9121 (m-30) cc_final: 0.8394 (p0) REVERT: 2 96 ILE cc_start: 0.8227 (mt) cc_final: 0.7822 (mm) REVERT: 2 98 PHE cc_start: 0.8807 (t80) cc_final: 0.8562 (t80) REVERT: 2 99 MET cc_start: 0.8601 (tpt) cc_final: 0.8095 (tmm) REVERT: 2 100 ASP cc_start: 0.8744 (m-30) cc_final: 0.8324 (m-30) REVERT: 2 101 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.8011 (mtt90) REVERT: 2 112 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8380 (tptp) REVERT: 3 30 GLN cc_start: 0.7945 (mt0) cc_final: 0.7728 (mt0) outliers start: 32 outliers final: 13 residues processed: 804 average time/residue: 0.4387 time to fit residues: 413.4105 Evaluate side-chains 586 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 573 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain Z residue 46 LEU Chi-restraints excluded: chain 2 residue 49 LEU Chi-restraints excluded: chain 2 residue 87 ARG Chi-restraints excluded: chain 3 residue 7 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN A 298 ASN A 332 HIS B 157 HIS B 179 GLN ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN B 233 ASN B 274 GLN B 281 GLN C 27 ASN C 120 HIS C 143 ASN C 281 ASN D 129 GLN D 164 GLN D 186 GLN D 236 ASN D 318 ASN H 15 ASN Z 6 GLN 2 45 GLN 2 106 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106214 restraints weight = 33999.880| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.66 r_work: 0.3175 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.674 21814 Z= 1.149 Angle : 0.949 18.694 30089 Z= 0.410 Chirality : 0.061 0.648 2914 Planarity : 0.007 0.053 3788 Dihedral : 18.459 114.342 3485 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.45 % Favored : 97.41 % Rotamer: Outliers : 4.36 % Allowed : 19.92 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.17), residues: 2203 helix: 0.28 (0.14), residues: 1243 sheet: 0.08 (0.64), residues: 54 loop : -1.46 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 127 TYR 0.019 0.002 TYR C 262 PHE 0.026 0.002 PHE T 8 TRP 0.043 0.002 TRP 2 92 HIS 0.008 0.002 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (21795) covalent geometry : angle 0.94855 / 0.41 (30089) hydrogen bonds : bond 0.06247 / 4.24 ( 970) hydrogen bonds : angle 4.88468 / 3.58 ( 2796) Misc. bond : bond 0.43197 / 31.23 ( 19) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 600 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.9202 (t80) cc_final: 0.8627 (t80) REVERT: A 65 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7676 (mm-30) REVERT: A 142 TRP cc_start: 0.8172 (m-10) cc_final: 0.7606 (m-10) REVERT: A 187 GLN cc_start: 0.9330 (tp40) cc_final: 0.8976 (tp40) REVERT: B 214 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8675 (mm) REVERT: B 230 ARG cc_start: 0.8469 (mmt-90) cc_final: 0.8251 (mmt90) REVERT: B 313 ASP cc_start: 0.9268 (t0) cc_final: 0.9037 (t0) REVERT: B 349 LYS cc_start: 0.9094 (tmmt) cc_final: 0.8557 (mttp) REVERT: B 350 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8386 (tm-30) REVERT: B 378 LYS cc_start: 0.9067 (mttp) cc_final: 0.8740 (mttp) REVERT: C 71 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8166 (mt-10) REVERT: C 141 ASP cc_start: 0.8775 (t0) cc_final: 0.8440 (t0) REVERT: C 193 ASP cc_start: 0.8220 (t0) cc_final: 0.7760 (t0) REVERT: C 409 SER cc_start: 0.8872 (t) cc_final: 0.8650 (p) REVERT: D 42 TYR cc_start: 0.9214 (t80) cc_final: 0.8999 (t80) REVERT: D 100 ASP cc_start: 0.8819 (t0) cc_final: 0.8357 (t0) REVERT: D 105 CYS cc_start: 0.9366 (m) cc_final: 0.9058 (m) REVERT: D 210 LEU cc_start: 0.9040 (mt) cc_final: 0.8824 (mt) REVERT: D 246 MET cc_start: 0.8887 (tpt) cc_final: 0.8610 (tpt) REVERT: D 263 ASN cc_start: 0.8505 (t0) cc_final: 0.8184 (t0) REVERT: D 297 ASP cc_start: 0.9240 (p0) cc_final: 0.9037 (p0) REVERT: D 318 ASN cc_start: 0.9298 (m-40) cc_final: 0.8853 (m110) REVERT: D 322 ASN cc_start: 0.8613 (m-40) cc_final: 0.8405 (m110) REVERT: E 62 SER cc_start: 0.8935 (m) cc_final: 0.8578 (p) REVERT: H 3 ARG cc_start: 0.8446 (ptm160) cc_final: 0.8184 (ptm-80) REVERT: K 18 PHE cc_start: 0.8074 (m-10) cc_final: 0.7798 (m-10) REVERT: L 7 ARG cc_start: 0.6941 (tmt170) cc_final: 0.6490 (tmt-80) REVERT: L 8 GLN cc_start: 0.8715 (mm110) cc_final: 0.8256 (mm110) REVERT: M 5 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6721 (pm20) REVERT: T 1 MET cc_start: 0.6889 (tpp) cc_final: 0.6076 (tpp) REVERT: T 24 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8297 (ptt90) REVERT: X 8 LYS cc_start: 0.8498 (mtpp) cc_final: 0.7973 (mtpp) REVERT: X 12 ILE cc_start: 0.9155 (mt) cc_final: 0.8905 (mp) REVERT: Z 37 LYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5863 (ttmm) REVERT: 2 23 LEU cc_start: 0.8616 (tt) cc_final: 0.8129 (mt) REVERT: 2 35 MET cc_start: 0.7571 (mpp) cc_final: 0.7232 (mpp) REVERT: 2 42 LYS cc_start: 0.8831 (tptt) cc_final: 0.8631 (mmmt) REVERT: 2 45 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8090 (pt0) REVERT: 2 71 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8263 (tppp) REVERT: 2 83 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7801 (p) REVERT: 2 96 ILE cc_start: 0.8539 (mt) cc_final: 0.8124 (mm) REVERT: 2 99 MET cc_start: 0.8812 (tpt) cc_final: 0.8295 (tmm) REVERT: 2 100 ASP cc_start: 0.9186 (m-30) cc_final: 0.8851 (m-30) REVERT: 2 111 GLN cc_start: 0.5916 (tm-30) cc_final: 0.5521 (tm-30) outliers start: 79 outliers final: 26 residues processed: 635 average time/residue: 0.4686 time to fit residues: 348.0318 Evaluate side-chains 573 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 541 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain Z residue 37 LYS Chi-restraints excluded: chain Z residue 46 LEU Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 68 VAL Chi-restraints excluded: chain 2 residue 71 LYS Chi-restraints excluded: chain 2 residue 83 THR Chi-restraints excluded: chain 3 residue 4 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 174 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 GLN B 338 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN 2 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092779 restraints weight = 34464.407| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.61 r_work: 0.2961 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.798 21814 Z= 0.278 Angle : 0.900 15.688 30089 Z= 0.401 Chirality : 0.058 0.701 2914 Planarity : 0.006 0.056 3788 Dihedral : 16.952 110.668 3462 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.54 % Favored : 96.41 % Rotamer: Outliers : 6.62 % Allowed : 19.70 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2203 helix: 0.91 (0.15), residues: 1233 sheet: 0.32 (0.65), residues: 54 loop : -1.00 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 124 TYR 0.022 0.002 TYR B 273 PHE 0.028 0.002 PHE B 246 TRP 0.019 0.002 TRP C 211 HIS 0.012 0.002 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.28 (21795) covalent geometry : angle 0.90013 / 0.40 (30089) hydrogen bonds : bond 0.06563 / 4.39 ( 970) hydrogen bonds : angle 4.65383 / 3.39 ( 2796) Misc. bond : bond 0.18478 / 8.82 ( 19) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 559 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7838 (mm-30) REVERT: A 132 GLU cc_start: 0.8925 (tt0) cc_final: 0.8556 (tt0) REVERT: A 187 GLN cc_start: 0.9317 (tp40) cc_final: 0.8741 (tp-100) REVERT: A 296 ASN cc_start: 0.9147 (m-40) cc_final: 0.8853 (t0) REVERT: A 334 ARG cc_start: 0.7393 (mpp-170) cc_final: 0.7010 (mpp-170) REVERT: B 101 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9095 (mp) REVERT: B 313 ASP cc_start: 0.9303 (t0) cc_final: 0.9066 (t0) REVERT: B 378 LYS cc_start: 0.9147 (mttp) cc_final: 0.8695 (mttm) REVERT: C 50 PHE cc_start: 0.9498 (t80) cc_final: 0.9262 (t80) REVERT: C 141 ASP cc_start: 0.8689 (t0) cc_final: 0.8171 (t0) REVERT: C 183 ASP cc_start: 0.8333 (t0) cc_final: 0.8011 (t0) REVERT: C 193 ASP cc_start: 0.8295 (t0) cc_final: 0.7893 (t0) REVERT: C 202 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9265 (mm) REVERT: C 350 ARG cc_start: 0.6127 (pmt170) cc_final: 0.2947 (mmt-90) REVERT: C 435 ARG cc_start: 0.8057 (mtp-110) cc_final: 0.7784 (ttm110) REVERT: D 42 TYR cc_start: 0.9294 (t80) cc_final: 0.9007 (t80) REVERT: D 100 ASP cc_start: 0.9149 (t0) cc_final: 0.8706 (t70) REVERT: D 210 LEU cc_start: 0.9001 (mt) cc_final: 0.8786 (mt) REVERT: D 246 MET cc_start: 0.9019 (tpt) cc_final: 0.8680 (tpt) REVERT: D 297 ASP cc_start: 0.9289 (p0) cc_final: 0.9065 (p0) REVERT: E 62 SER cc_start: 0.9136 (m) cc_final: 0.8791 (p) REVERT: E 74 GLN cc_start: 0.7982 (pm20) cc_final: 0.7345 (pm20) REVERT: E 80 LEU cc_start: 0.8878 (mt) cc_final: 0.8443 (mt) REVERT: F 44 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7342 (mp10) REVERT: H 3 ARG cc_start: 0.8641 (ptm160) cc_final: 0.8416 (ptp-170) REVERT: I 6 ILE cc_start: 0.8836 (pp) cc_final: 0.8629 (pp) REVERT: I 10 ILE cc_start: 0.9382 (mt) cc_final: 0.9162 (mm) REVERT: K 18 PHE cc_start: 0.8161 (m-10) cc_final: 0.7872 (m-10) REVERT: T 1 MET cc_start: 0.7117 (tpp) cc_final: 0.6460 (tpp) REVERT: X 8 LYS cc_start: 0.8516 (mtpp) cc_final: 0.8097 (mtpp) REVERT: X 12 ILE cc_start: 0.9219 (mt) cc_final: 0.8951 (mp) REVERT: y 27 MET cc_start: 0.8149 (tmm) cc_final: 0.7336 (tmm) REVERT: Z 6 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8047 (mp10) REVERT: Z 17 PHE cc_start: 0.8846 (t80) cc_final: 0.8619 (t80) REVERT: Z 34 ASP cc_start: 0.9086 (m-30) cc_final: 0.8800 (m-30) REVERT: 2 4 MET cc_start: 0.1784 (pmm) cc_final: 0.1254 (ptt) REVERT: 2 15 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7906 (mm-30) REVERT: 2 22 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.6238 (tpm170) REVERT: 2 23 LEU cc_start: 0.8574 (tt) cc_final: 0.8206 (mt) REVERT: 2 35 MET cc_start: 0.7823 (mpp) cc_final: 0.7425 (mpp) REVERT: 2 42 LYS cc_start: 0.8875 (tptt) cc_final: 0.8635 (mmmt) REVERT: 2 43 ILE cc_start: 0.8551 (tp) cc_final: 0.8271 (tt) REVERT: 2 60 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6702 (mt-10) REVERT: 2 99 MET cc_start: 0.8972 (tpt) cc_final: 0.8477 (tmt) REVERT: 2 100 ASP cc_start: 0.9205 (m-30) cc_final: 0.8866 (p0) REVERT: 3 24 GLN cc_start: 0.8198 (pm20) cc_final: 0.7924 (mp10) outliers start: 120 outliers final: 52 residues processed: 610 average time/residue: 0.4444 time to fit residues: 315.1048 Evaluate side-chains 564 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 508 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain Z residue 6 GLN Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 46 LEU Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 2 residue 22 ARG Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 68 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 183 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 GLN B 157 HIS B 289 GLN C 299 GLN C 315 ASN C 403 ASN D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094429 restraints weight = 34247.933| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.59 r_work: 0.2978 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.839 21814 Z= 0.191 Angle : 0.758 14.068 30089 Z= 0.344 Chirality : 0.050 0.415 2914 Planarity : 0.005 0.043 3788 Dihedral : 16.432 102.870 3462 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.35 % Allowed : 23.29 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 2203 helix: 1.27 (0.15), residues: 1233 sheet: 0.27 (0.69), residues: 48 loop : -0.82 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 476 TYR 0.040 0.002 TYR C 328 PHE 0.024 0.001 PHE X 10 TRP 0.016 0.001 TRP Z 33 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (21795) covalent geometry : angle 0.75774 / 0.34 (30089) hydrogen bonds : bond 0.05476 / 3.70 ( 970) hydrogen bonds : angle 4.40157 / 3.22 ( 2796) Misc. bond : bond 0.19314 / 9.21 ( 19) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 534 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7888 (mm-30) REVERT: A 140 ARG cc_start: 0.8588 (ttp80) cc_final: 0.8337 (ttp80) REVERT: A 142 TRP cc_start: 0.8391 (m-10) cc_final: 0.7709 (m-10) REVERT: A 187 GLN cc_start: 0.9324 (tp40) cc_final: 0.9101 (tm-30) REVERT: A 225 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8301 (ptp-170) REVERT: B 313 ASP cc_start: 0.9241 (t0) cc_final: 0.9015 (t0) REVERT: B 349 LYS cc_start: 0.9097 (tmmt) cc_final: 0.8696 (mttp) REVERT: B 378 LYS cc_start: 0.9133 (mttp) cc_final: 0.8669 (mttm) REVERT: C 141 ASP cc_start: 0.8636 (t0) cc_final: 0.8001 (t0) REVERT: C 183 ASP cc_start: 0.8423 (t0) cc_final: 0.7961 (t0) REVERT: C 193 ASP cc_start: 0.8224 (t0) cc_final: 0.7723 (t0) REVERT: C 342 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7796 (tt0) REVERT: C 350 ARG cc_start: 0.5916 (pmt170) cc_final: 0.2715 (mmt-90) REVERT: C 371 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8457 (t70) REVERT: C 384 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.9030 (tmm) REVERT: C 435 ARG cc_start: 0.7983 (mtp-110) cc_final: 0.7629 (ttm110) REVERT: D 42 TYR cc_start: 0.9311 (t80) cc_final: 0.9012 (t80) REVERT: D 100 ASP cc_start: 0.9066 (t0) cc_final: 0.8592 (t70) REVERT: D 210 LEU cc_start: 0.8977 (mt) cc_final: 0.8767 (mt) REVERT: D 295 SER cc_start: 0.9321 (p) cc_final: 0.9100 (p) REVERT: D 297 ASP cc_start: 0.9260 (p0) cc_final: 0.9032 (p0) REVERT: D 307 GLU cc_start: 0.7428 (pp20) cc_final: 0.7158 (pp20) REVERT: E 58 GLN cc_start: 0.7356 (tp-100) cc_final: 0.7108 (tp-100) REVERT: E 62 SER cc_start: 0.9158 (m) cc_final: 0.8771 (p) REVERT: E 71 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7872 (mm-30) REVERT: E 74 GLN cc_start: 0.8082 (pm20) cc_final: 0.7841 (pm20) REVERT: E 77 GLU cc_start: 0.8775 (tp30) cc_final: 0.8569 (mt-10) REVERT: E 80 LEU cc_start: 0.8800 (mt) cc_final: 0.8569 (mt) REVERT: F 44 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7352 (mp10) REVERT: I 5 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8095 (tttp) REVERT: K 18 PHE cc_start: 0.8211 (m-10) cc_final: 0.7882 (m-10) REVERT: L 7 ARG cc_start: 0.7443 (tmt170) cc_final: 0.6862 (tmt-80) REVERT: L 8 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8226 (mp10) REVERT: M 30 GLU cc_start: 0.7532 (pp20) cc_final: 0.7155 (OUTLIER) REVERT: T 1 MET cc_start: 0.7232 (tpp) cc_final: 0.6600 (tpp) REVERT: T 5 THR cc_start: 0.8985 (m) cc_final: 0.8678 (p) REVERT: X 8 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8103 (mtpp) REVERT: X 12 ILE cc_start: 0.9207 (mt) cc_final: 0.8962 (mp) REVERT: Z 6 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8036 (mp10) REVERT: 2 4 MET cc_start: 0.1673 (pmm) cc_final: 0.1214 (ptt) REVERT: 2 15 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7853 (mm-30) REVERT: 2 23 LEU cc_start: 0.8490 (tt) cc_final: 0.8078 (pp) REVERT: 2 25 ARG cc_start: 0.7580 (tpp80) cc_final: 0.7154 (tpt90) REVERT: 2 35 MET cc_start: 0.7935 (mpp) cc_final: 0.7563 (mpp) REVERT: 2 42 LYS cc_start: 0.8917 (tptt) cc_final: 0.8699 (mmmt) REVERT: 2 43 ILE cc_start: 0.8649 (tp) cc_final: 0.8353 (tt) REVERT: 2 60 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6662 (mt-10) REVERT: 2 83 THR cc_start: 0.8515 (m) cc_final: 0.8127 (p) REVERT: 2 94 ARG cc_start: 0.8279 (tpt-90) cc_final: 0.8021 (tpt170) REVERT: 2 96 ILE cc_start: 0.8516 (mm) cc_final: 0.8223 (mm) REVERT: 2 99 MET cc_start: 0.8982 (tpt) cc_final: 0.8523 (tmt) REVERT: 2 100 ASP cc_start: 0.9210 (m-30) cc_final: 0.8878 (p0) REVERT: 2 114 GLU cc_start: 0.8311 (mp0) cc_final: 0.7847 (mm-30) REVERT: 3 7 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5702 (pm20) REVERT: 3 24 GLN cc_start: 0.8184 (pm20) cc_final: 0.7902 (mp10) outliers start: 115 outliers final: 49 residues processed: 589 average time/residue: 0.5159 time to fit residues: 354.4697 Evaluate side-chains 560 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 506 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain Z residue 6 GLN Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 46 LEU Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 68 VAL Chi-restraints excluded: chain 3 residue 7 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 66 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 25 optimal weight: 0.0970 chunk 206 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.096845 restraints weight = 34039.816| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.63 r_work: 0.3018 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.843 21814 Z= 0.130 Angle : 0.682 14.837 30089 Z= 0.314 Chirality : 0.045 0.347 2914 Planarity : 0.005 0.042 3788 Dihedral : 15.544 86.964 3459 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.24 % Allowed : 24.50 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.18), residues: 2203 helix: 1.55 (0.15), residues: 1235 sheet: 0.39 (0.71), residues: 48 loop : -0.65 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 476 TYR 0.013 0.001 TYR B 279 PHE 0.020 0.001 PHE X 10 TRP 0.023 0.001 TRP Z 33 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (21795) covalent geometry : angle 0.68187 / 0.31 (30089) hydrogen bonds : bond 0.04605 / 3.14 ( 970) hydrogen bonds : angle 4.16305 / 3.04 ( 2796) Misc. bond : bond 0.19354 / 9.22 ( 19) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 538 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 142 TRP cc_start: 0.8271 (m-10) cc_final: 0.7486 (m-10) REVERT: A 225 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8257 (ptp-170) REVERT: B 130 GLU cc_start: 0.8858 (mp0) cc_final: 0.8594 (mp0) REVERT: B 349 LYS cc_start: 0.9066 (tmmt) cc_final: 0.8805 (mttt) REVERT: B 378 LYS cc_start: 0.9118 (mttp) cc_final: 0.8640 (mttm) REVERT: B 442 ILE cc_start: 0.8755 (mm) cc_final: 0.8490 (OUTLIER) REVERT: C 74 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8473 (mm) REVERT: C 141 ASP cc_start: 0.8508 (t0) cc_final: 0.7902 (t0) REVERT: C 183 ASP cc_start: 0.8485 (t0) cc_final: 0.7921 (t0) REVERT: C 193 ASP cc_start: 0.8278 (t0) cc_final: 0.7778 (t0) REVERT: C 342 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7694 (tt0) REVERT: C 435 ARG cc_start: 0.7928 (mtp-110) cc_final: 0.7726 (ttm110) REVERT: C 437 ARG cc_start: 0.7598 (mmm160) cc_final: 0.7211 (mmm160) REVERT: D 100 ASP cc_start: 0.9026 (t0) cc_final: 0.8583 (t70) REVERT: D 210 LEU cc_start: 0.8940 (mt) cc_final: 0.8724 (mt) REVERT: D 244 TYR cc_start: 0.9521 (p90) cc_final: 0.9249 (p90) REVERT: E 62 SER cc_start: 0.9079 (m) cc_final: 0.8649 (p) REVERT: E 71 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7870 (mm-30) REVERT: E 77 GLU cc_start: 0.8888 (tp30) cc_final: 0.8575 (mt-10) REVERT: E 80 LEU cc_start: 0.8813 (mt) cc_final: 0.8573 (mt) REVERT: F 44 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7416 (mp10) REVERT: H 7 LEU cc_start: 0.9357 (tp) cc_final: 0.9053 (tt) REVERT: H 17 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7900 (mm-30) REVERT: L 7 ARG cc_start: 0.7413 (tmt170) cc_final: 0.6871 (tmt-80) REVERT: L 8 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8151 (mp10) REVERT: M 27 VAL cc_start: 0.9294 (t) cc_final: 0.8963 (t) REVERT: M 30 GLU cc_start: 0.7638 (pp20) cc_final: 0.7197 (OUTLIER) REVERT: T 1 MET cc_start: 0.7226 (tpp) cc_final: 0.6539 (tpp) REVERT: T 5 THR cc_start: 0.8885 (m) cc_final: 0.8681 (p) REVERT: T 24 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8049 (ptt-90) REVERT: T 25 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7681 (mt-10) REVERT: X 8 LYS cc_start: 0.8550 (mtpp) cc_final: 0.8108 (mtpp) REVERT: X 12 ILE cc_start: 0.9206 (mt) cc_final: 0.8951 (mp) REVERT: y 27 MET cc_start: 0.8255 (tmm) cc_final: 0.7353 (tmm) REVERT: Z 6 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8273 (mt0) REVERT: Z 17 PHE cc_start: 0.8874 (t80) cc_final: 0.8619 (t80) REVERT: 2 15 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7112 (tp30) REVERT: 2 16 GLU cc_start: 0.8544 (pm20) cc_final: 0.8129 (pm20) REVERT: 2 23 LEU cc_start: 0.8359 (tt) cc_final: 0.8060 (pp) REVERT: 2 25 ARG cc_start: 0.7591 (tpp80) cc_final: 0.7319 (ttt90) REVERT: 2 35 MET cc_start: 0.7976 (mpp) cc_final: 0.7492 (mpp) REVERT: 2 42 LYS cc_start: 0.8897 (tptt) cc_final: 0.8613 (mmmt) REVERT: 2 43 ILE cc_start: 0.8594 (tp) cc_final: 0.8244 (tt) REVERT: 2 60 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6188 (mt-10) REVERT: 2 96 ILE cc_start: 0.8513 (mm) cc_final: 0.8252 (mm) REVERT: 2 99 MET cc_start: 0.8956 (tpt) cc_final: 0.8512 (tmt) REVERT: 2 100 ASP cc_start: 0.9175 (m-30) cc_final: 0.8858 (p0) REVERT: 2 114 GLU cc_start: 0.8216 (mp0) cc_final: 0.8009 (mp0) REVERT: 3 7 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5687 (pm20) REVERT: 3 24 GLN cc_start: 0.8159 (pm20) cc_final: 0.7765 (mp10) outliers start: 95 outliers final: 45 residues processed: 579 average time/residue: 0.4841 time to fit residues: 326.5228 Evaluate side-chains 556 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 507 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain Z residue 6 GLN Chi-restraints excluded: chain Z residue 46 LEU Chi-restraints excluded: chain Z residue 58 ASN Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 68 VAL Chi-restraints excluded: chain 3 residue 7 GLU Chi-restraints excluded: chain 3 residue 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 99 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 120 optimal weight: 0.0980 chunk 199 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN C 315 ASN C 403 ASN D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN K 40 GLN Z 58 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097347 restraints weight = 34094.368| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.63 r_work: 0.3034 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.912 21814 Z= 0.131 Angle : 0.683 14.537 30089 Z= 0.315 Chirality : 0.044 0.288 2914 Planarity : 0.005 0.051 3788 Dihedral : 15.019 89.669 3459 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.80 % Allowed : 25.17 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 2203 helix: 1.68 (0.15), residues: 1232 sheet: 0.64 (0.74), residues: 48 loop : -0.57 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG 2 94 TYR 0.014 0.001 TYR B 226 PHE 0.023 0.001 PHE A 274 TRP 0.022 0.001 TRP Z 33 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (21795) covalent geometry : angle 0.68310 / 0.32 (30089) hydrogen bonds : bond 0.04377 / 2.97 ( 970) hydrogen bonds : angle 4.08042 / 2.98 ( 2796) Misc. bond : bond 0.20929 / 9.97 ( 19) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 531 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7959 (mm-30) REVERT: A 132 GLU cc_start: 0.8911 (tt0) cc_final: 0.8556 (tt0) REVERT: A 142 TRP cc_start: 0.8297 (m-10) cc_final: 0.7467 (m-10) REVERT: B 350 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8363 (tm-30) REVERT: B 378 LYS cc_start: 0.9131 (mttp) cc_final: 0.8804 (mttp) REVERT: B 409 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8078 (mm-40) REVERT: C 128 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8144 (mp) REVERT: C 183 ASP cc_start: 0.8518 (t0) cc_final: 0.8247 (t0) REVERT: C 193 ASP cc_start: 0.8276 (t0) cc_final: 0.7792 (t0) REVERT: C 277 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8632 (t80) REVERT: C 342 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7724 (tt0) REVERT: C 350 ARG cc_start: 0.5913 (pmt170) cc_final: 0.2589 (mmt-90) REVERT: C 435 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.7675 (ttm110) REVERT: C 437 ARG cc_start: 0.7611 (mmm160) cc_final: 0.7234 (mmm160) REVERT: D 100 ASP cc_start: 0.9016 (t0) cc_final: 0.8569 (t70) REVERT: D 210 LEU cc_start: 0.8920 (mt) cc_final: 0.8704 (mt) REVERT: D 244 TYR cc_start: 0.9516 (p90) cc_final: 0.9300 (p90) REVERT: E 62 SER cc_start: 0.9075 (m) cc_final: 0.8648 (p) REVERT: E 71 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8112 (mm-30) REVERT: E 77 GLU cc_start: 0.8920 (tp30) cc_final: 0.8590 (mt-10) REVERT: E 80 LEU cc_start: 0.8858 (mt) cc_final: 0.8588 (mt) REVERT: F 44 GLN cc_start: 0.8107 (mm-40) cc_final: 0.7425 (mp10) REVERT: H 4 ARG cc_start: 0.9203 (mmm-85) cc_final: 0.8911 (mmm-85) REVERT: H 7 LEU cc_start: 0.9364 (tp) cc_final: 0.9065 (tt) REVERT: H 17 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7832 (mm-30) REVERT: H 31 MET cc_start: 0.9087 (ttp) cc_final: 0.8759 (ttm) REVERT: L 7 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6873 (tmt-80) REVERT: L 8 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8144 (mp10) REVERT: T 1 MET cc_start: 0.7288 (tpp) cc_final: 0.6660 (tpp) REVERT: X 8 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8120 (mtpp) REVERT: X 36 LYS cc_start: 0.6650 (pmtt) cc_final: 0.6322 (pptt) REVERT: Z 6 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: 2 25 ARG cc_start: 0.7552 (tpp80) cc_final: 0.7245 (ttt90) REVERT: 2 35 MET cc_start: 0.8001 (mpp) cc_final: 0.7613 (mpp) REVERT: 2 42 LYS cc_start: 0.8879 (tptt) cc_final: 0.8624 (mmmt) REVERT: 2 43 ILE cc_start: 0.8617 (tp) cc_final: 0.8255 (tt) REVERT: 2 96 ILE cc_start: 0.8553 (mm) cc_final: 0.8260 (mm) REVERT: 2 99 MET cc_start: 0.8863 (tpt) cc_final: 0.8354 (tmt) REVERT: 2 100 ASP cc_start: 0.9114 (m-30) cc_final: 0.8873 (m-30) REVERT: 2 111 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7366 (pp30) REVERT: 3 7 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5669 (pm20) REVERT: 3 10 ARG cc_start: 0.6850 (mpt90) cc_final: 0.6555 (mpt90) REVERT: 3 24 GLN cc_start: 0.7931 (pm20) cc_final: 0.7680 (mp10) outliers start: 87 outliers final: 44 residues processed: 570 average time/residue: 0.4680 time to fit residues: 311.2704 Evaluate side-chains 559 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 508 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 7 ARG Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain Z residue 6 GLN Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 68 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 7 GLU Chi-restraints excluded: chain 3 residue 53 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 113 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 100 optimal weight: 0.0670 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN K 40 GLN Z 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096195 restraints weight = 34260.376| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.64 r_work: 0.3016 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.926 21814 Z= 0.148 Angle : 0.696 14.885 30089 Z= 0.323 Chirality : 0.045 0.293 2914 Planarity : 0.005 0.069 3788 Dihedral : 14.804 89.471 3457 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.02 % Allowed : 25.66 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.18), residues: 2203 helix: 1.72 (0.15), residues: 1231 sheet: 0.74 (0.76), residues: 48 loop : -0.52 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 476 TYR 0.012 0.001 TYR B 279 PHE 0.024 0.001 PHE A 274 TRP 0.028 0.001 TRP Z 33 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (21795) covalent geometry : angle 0.69594 / 0.32 (30089) hydrogen bonds : bond 0.04565 / 3.09 ( 970) hydrogen bonds : angle 4.09064 / 3.00 ( 2796) Misc. bond : bond 0.21249 / 10.12 ( 19) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 513 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7864 (mm-30) REVERT: A 242 GLU cc_start: 0.8516 (mp0) cc_final: 0.8041 (mp0) REVERT: B 130 GLU cc_start: 0.8802 (mp0) cc_final: 0.8570 (mp0) REVERT: B 409 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8085 (mm-40) REVERT: C 128 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8170 (mp) REVERT: C 183 ASP cc_start: 0.8548 (t0) cc_final: 0.8267 (t0) REVERT: C 193 ASP cc_start: 0.8295 (t0) cc_final: 0.7819 (t0) REVERT: C 277 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8671 (t80) REVERT: C 342 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7697 (tt0) REVERT: C 350 ARG cc_start: 0.5961 (pmt170) cc_final: 0.2668 (mmt-90) REVERT: C 355 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8258 (mm-30) REVERT: C 435 ARG cc_start: 0.7881 (mtp-110) cc_final: 0.7673 (ttm110) REVERT: C 437 ARG cc_start: 0.7633 (mmm160) cc_final: 0.7256 (mmm160) REVERT: D 100 ASP cc_start: 0.9036 (t0) cc_final: 0.8504 (t0) REVERT: D 210 LEU cc_start: 0.8937 (mt) cc_final: 0.8722 (mt) REVERT: D 244 TYR cc_start: 0.9540 (p90) cc_final: 0.9290 (p90) REVERT: D 251 ARG cc_start: 0.9030 (ttt90) cc_final: 0.8815 (ttm170) REVERT: E 62 SER cc_start: 0.9071 (m) cc_final: 0.8639 (p) REVERT: E 71 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8162 (mm-30) REVERT: E 77 GLU cc_start: 0.8939 (tp30) cc_final: 0.8572 (mt-10) REVERT: E 80 LEU cc_start: 0.8806 (mt) cc_final: 0.8534 (mt) REVERT: F 44 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7455 (mp10) REVERT: H 7 LEU cc_start: 0.9381 (tp) cc_final: 0.9081 (tt) REVERT: H 17 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7770 (mm-30) REVERT: H 31 MET cc_start: 0.9110 (ttp) cc_final: 0.8880 (ttm) REVERT: L 7 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6817 (mtp85) REVERT: L 8 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8196 (mp10) REVERT: M 30 GLU cc_start: 0.8276 (tp30) cc_final: 0.7971 (OUTLIER) REVERT: T 1 MET cc_start: 0.7553 (tpp) cc_final: 0.6841 (tpp) REVERT: T 24 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8056 (ptt-90) REVERT: X 36 LYS cc_start: 0.6655 (pmtt) cc_final: 0.6344 (pptt) REVERT: Z 6 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: 2 15 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7649 (tp30) REVERT: 2 16 GLU cc_start: 0.8562 (pm20) cc_final: 0.8181 (pm20) REVERT: 2 25 ARG cc_start: 0.7521 (tpp80) cc_final: 0.7308 (ttt90) REVERT: 2 35 MET cc_start: 0.8000 (mpp) cc_final: 0.7609 (mpp) REVERT: 2 42 LYS cc_start: 0.8837 (tptt) cc_final: 0.8556 (mmmt) REVERT: 2 43 ILE cc_start: 0.8579 (tp) cc_final: 0.8283 (tt) REVERT: 2 71 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8366 (tppp) REVERT: 2 96 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8213 (mm) REVERT: 2 99 MET cc_start: 0.8870 (tpt) cc_final: 0.8402 (tmt) REVERT: 2 100 ASP cc_start: 0.9095 (m-30) cc_final: 0.8875 (m-30) REVERT: 2 111 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7367 (pp30) REVERT: 3 7 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5626 (pm20) REVERT: 3 24 GLN cc_start: 0.7917 (pm20) cc_final: 0.7659 (mp10) outliers start: 91 outliers final: 55 residues processed: 555 average time/residue: 0.4671 time to fit residues: 302.1172 Evaluate side-chains 561 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 497 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 7 ARG Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain Z residue 6 GLN Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 68 VAL Chi-restraints excluded: chain 2 residue 71 LYS Chi-restraints excluded: chain 2 residue 96 ILE Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 7 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 159 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 123 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN K 40 GLN y 21 GLN Z 38 GLN Z 58 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094504 restraints weight = 33901.700| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.61 r_work: 0.2969 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.965 21814 Z= 0.161 Angle : 0.714 15.115 30089 Z= 0.332 Chirality : 0.045 0.262 2914 Planarity : 0.005 0.066 3788 Dihedral : 14.667 89.705 3457 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.97 % Allowed : 26.66 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.18), residues: 2203 helix: 1.70 (0.15), residues: 1230 sheet: 0.79 (0.76), residues: 48 loop : -0.42 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 127 TYR 0.034 0.001 TYR C 328 PHE 0.027 0.001 PHE A 274 TRP 0.034 0.001 TRP Z 33 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (21795) covalent geometry : angle 0.71447 / 0.33 (30089) hydrogen bonds : bond 0.04826 / 3.25 ( 970) hydrogen bonds : angle 4.13916 / 3.03 ( 2796) Misc. bond : bond 0.22165 / 10.56 ( 19) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 499 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 142 TRP cc_start: 0.8296 (m-10) cc_final: 0.7414 (m-10) REVERT: A 242 GLU cc_start: 0.8509 (mp0) cc_final: 0.8043 (mp0) REVERT: B 130 GLU cc_start: 0.8834 (mp0) cc_final: 0.8600 (mp0) REVERT: B 409 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8177 (mm-40) REVERT: C 74 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7990 (mm) REVERT: C 141 ASP cc_start: 0.8405 (t0) cc_final: 0.7790 (t0) REVERT: C 183 ASP cc_start: 0.8588 (t0) cc_final: 0.8376 (t0) REVERT: C 193 ASP cc_start: 0.8298 (t0) cc_final: 0.7805 (t0) REVERT: C 342 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7726 (tt0) REVERT: C 350 ARG cc_start: 0.5808 (pmt170) cc_final: 0.2556 (mmt-90) REVERT: C 355 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8283 (mm-30) REVERT: C 435 ARG cc_start: 0.7845 (mtp-110) cc_final: 0.7601 (ttm110) REVERT: C 437 ARG cc_start: 0.7587 (mmm160) cc_final: 0.7223 (mmm160) REVERT: D 100 ASP cc_start: 0.9018 (t0) cc_final: 0.8456 (t0) REVERT: D 244 TYR cc_start: 0.9536 (p90) cc_final: 0.9282 (p90) REVERT: E 58 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6706 (tp40) REVERT: E 62 SER cc_start: 0.9119 (m) cc_final: 0.8675 (p) REVERT: E 71 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8284 (mm-30) REVERT: E 77 GLU cc_start: 0.8958 (tp30) cc_final: 0.8573 (mt-10) REVERT: E 80 LEU cc_start: 0.8800 (mt) cc_final: 0.8524 (mt) REVERT: F 44 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7440 (mp10) REVERT: H 17 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7724 (mm-30) REVERT: H 31 MET cc_start: 0.9095 (ttp) cc_final: 0.8817 (ttm) REVERT: L 7 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6737 (mtp85) REVERT: M 30 GLU cc_start: 0.8304 (tp30) cc_final: 0.7998 (pp20) REVERT: T 1 MET cc_start: 0.7364 (tpp) cc_final: 0.6737 (tpp) REVERT: T 24 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8220 (ptm-80) REVERT: X 36 LYS cc_start: 0.6598 (pmtt) cc_final: 0.6383 (pptt) REVERT: 2 6 GLU cc_start: 0.5529 (mm-30) cc_final: 0.5226 (mm-30) REVERT: 2 16 GLU cc_start: 0.8638 (pm20) cc_final: 0.8312 (pm20) REVERT: 2 23 LEU cc_start: 0.8148 (tm) cc_final: 0.7834 (pp) REVERT: 2 25 ARG cc_start: 0.7534 (tpp80) cc_final: 0.7298 (ttt90) REVERT: 2 35 MET cc_start: 0.8010 (mpp) cc_final: 0.7575 (mpp) REVERT: 2 42 LYS cc_start: 0.8779 (tptt) cc_final: 0.8382 (mmpt) REVERT: 2 43 ILE cc_start: 0.8644 (tp) cc_final: 0.8353 (tt) REVERT: 2 60 GLU cc_start: 0.7459 (tt0) cc_final: 0.6598 (pp20) REVERT: 2 71 LYS cc_start: 0.8629 (tppp) cc_final: 0.8343 (tppp) REVERT: 2 96 ILE cc_start: 0.8491 (mm) cc_final: 0.8182 (mm) REVERT: 2 99 MET cc_start: 0.8881 (tpt) cc_final: 0.8393 (tmt) REVERT: 2 100 ASP cc_start: 0.9098 (m-30) cc_final: 0.8873 (m-30) REVERT: 2 111 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7315 (pp30) REVERT: 3 7 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5789 (pm20) REVERT: 3 24 GLN cc_start: 0.7903 (pm20) cc_final: 0.7648 (mp10) outliers start: 90 outliers final: 51 residues processed: 541 average time/residue: 0.4845 time to fit residues: 305.0126 Evaluate side-chains 550 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 492 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 7 ARG Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 68 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 7 GLU Chi-restraints excluded: chain 3 residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 161 optimal weight: 0.7980 chunk 203 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN H 15 ASN ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.130823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.096071 restraints weight = 33953.233| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.65 r_work: 0.2997 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.957 21814 Z= 0.135 Angle : 0.706 14.937 30089 Z= 0.330 Chirality : 0.044 0.250 2914 Planarity : 0.004 0.057 3788 Dihedral : 14.448 87.576 3457 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.08 % Allowed : 27.70 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.18), residues: 2203 helix: 1.71 (0.15), residues: 1223 sheet: 0.87 (0.77), residues: 48 loop : -0.41 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 476 TYR 0.029 0.001 TYR C 328 PHE 0.029 0.001 PHE Z 17 TRP 0.044 0.001 TRP Z 33 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (21795) covalent geometry : angle 0.70598 / 0.33 (30089) hydrogen bonds : bond 0.04434 / 3.01 ( 970) hydrogen bonds : angle 4.09559 / 3.00 ( 2796) Misc. bond : bond 0.21964 / 10.46 ( 19) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 503 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7813 (mm-30) REVERT: A 132 GLU cc_start: 0.8947 (tt0) cc_final: 0.8549 (tt0) REVERT: A 142 TRP cc_start: 0.8204 (m-10) cc_final: 0.7272 (m-10) REVERT: A 329 GLU cc_start: 0.8792 (tt0) cc_final: 0.8589 (tm-30) REVERT: B 119 ASP cc_start: 0.8654 (p0) cc_final: 0.8349 (p0) REVERT: B 130 GLU cc_start: 0.8853 (mp0) cc_final: 0.8612 (mp0) REVERT: B 409 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8145 (mm-40) REVERT: C 183 ASP cc_start: 0.8605 (t0) cc_final: 0.8400 (t0) REVERT: C 193 ASP cc_start: 0.8294 (t0) cc_final: 0.7823 (t0) REVERT: C 299 GLN cc_start: 0.9084 (mm110) cc_final: 0.8831 (mm110) REVERT: C 342 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7748 (tt0) REVERT: C 350 ARG cc_start: 0.5875 (pmt170) cc_final: 0.2555 (mmt-90) REVERT: C 355 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8285 (mm-30) REVERT: C 435 ARG cc_start: 0.7852 (mtp-110) cc_final: 0.7510 (ttm110) REVERT: D 100 ASP cc_start: 0.9002 (t0) cc_final: 0.8531 (t70) REVERT: D 186 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8817 (tp-100) REVERT: D 244 TYR cc_start: 0.9505 (p90) cc_final: 0.9233 (p90) REVERT: D 334 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8889 (mt0) REVERT: E 42 LEU cc_start: 0.8913 (tp) cc_final: 0.8513 (tp) REVERT: E 62 SER cc_start: 0.9066 (m) cc_final: 0.8600 (p) REVERT: E 71 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8337 (mm-30) REVERT: E 77 GLU cc_start: 0.8931 (tp30) cc_final: 0.8721 (tp30) REVERT: E 80 LEU cc_start: 0.8804 (mt) cc_final: 0.8518 (mt) REVERT: F 44 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7425 (mp10) REVERT: H 7 LEU cc_start: 0.9427 (tp) cc_final: 0.9110 (tt) REVERT: H 17 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: H 31 MET cc_start: 0.9053 (ttp) cc_final: 0.8816 (ttm) REVERT: L 7 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6723 (tmt-80) REVERT: L 8 GLN cc_start: 0.8670 (mm-40) cc_final: 0.7847 (mt0) REVERT: M 30 GLU cc_start: 0.8295 (tp30) cc_final: 0.8064 (pp20) REVERT: T 1 MET cc_start: 0.7154 (tpp) cc_final: 0.6434 (tpp) REVERT: T 24 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8068 (ptm-80) REVERT: 2 15 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7553 (tp30) REVERT: 2 23 LEU cc_start: 0.8072 (tm) cc_final: 0.7736 (pp) REVERT: 2 25 ARG cc_start: 0.7523 (tpp80) cc_final: 0.7287 (ttt90) REVERT: 2 35 MET cc_start: 0.8009 (mpp) cc_final: 0.7679 (mpp) REVERT: 2 43 ILE cc_start: 0.8758 (tp) cc_final: 0.8466 (tt) REVERT: 2 56 MET cc_start: 0.8954 (mtm) cc_final: 0.8698 (mtm) REVERT: 2 60 GLU cc_start: 0.7475 (tt0) cc_final: 0.6840 (pp20) REVERT: 2 71 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8284 (tppp) REVERT: 2 94 ARG cc_start: 0.7513 (tpm170) cc_final: 0.6797 (tpm170) REVERT: 2 96 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8243 (mm) REVERT: 2 99 MET cc_start: 0.8855 (tpt) cc_final: 0.8423 (tmt) REVERT: 2 100 ASP cc_start: 0.9090 (m-30) cc_final: 0.8786 (p0) REVERT: 2 111 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7271 (pp30) REVERT: 3 7 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5769 (pm20) REVERT: 3 10 ARG cc_start: 0.6822 (mpt90) cc_final: 0.6505 (mpt90) REVERT: 3 24 GLN cc_start: 0.7918 (pm20) cc_final: 0.7698 (mp10) outliers start: 74 outliers final: 45 residues processed: 533 average time/residue: 0.5113 time to fit residues: 316.9572 Evaluate side-chains 542 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 489 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 334 GLN Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 7 ARG Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 49 LEU Chi-restraints excluded: chain 2 residue 68 VAL Chi-restraints excluded: chain 2 residue 71 LYS Chi-restraints excluded: chain 2 residue 96 ILE Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 7 GLU Chi-restraints excluded: chain 3 residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 49 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 106 optimal weight: 0.0270 chunk 209 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN K 40 GLN ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN ** 2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.131162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.096532 restraints weight = 34158.380| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.64 r_work: 0.2999 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.926 21814 Z= 0.137 Angle : 0.715 15.014 30089 Z= 0.334 Chirality : 0.044 0.298 2914 Planarity : 0.005 0.052 3788 Dihedral : 14.293 85.726 3455 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.15 % Allowed : 28.97 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.18), residues: 2203 helix: 1.68 (0.15), residues: 1228 sheet: -0.15 (0.70), residues: 58 loop : -0.36 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 476 TYR 0.028 0.001 TYR C 328 PHE 0.027 0.001 PHE A 274 TRP 0.044 0.001 TRP Z 33 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (21795) covalent geometry : angle 0.71472 / 0.33 (30089) hydrogen bonds : bond 0.04389 / 2.96 ( 970) hydrogen bonds : angle 4.11497 / 3.03 ( 2796) Misc. bond : bond 0.21254 / 10.12 ( 19) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 496 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7723 (mm-30) REVERT: A 132 GLU cc_start: 0.8909 (tt0) cc_final: 0.8509 (tt0) REVERT: A 142 TRP cc_start: 0.8136 (m-10) cc_final: 0.7248 (m-10) REVERT: B 119 ASP cc_start: 0.8645 (p0) cc_final: 0.8341 (p0) REVERT: B 130 GLU cc_start: 0.8866 (mp0) cc_final: 0.8650 (mp0) REVERT: B 409 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8157 (mm-40) REVERT: C 50 PHE cc_start: 0.9404 (t80) cc_final: 0.9169 (t80) REVERT: C 193 ASP cc_start: 0.8304 (t0) cc_final: 0.7824 (t0) REVERT: C 299 GLN cc_start: 0.9090 (mm110) cc_final: 0.8853 (mm110) REVERT: C 342 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7714 (tt0) REVERT: C 350 ARG cc_start: 0.5877 (pmt170) cc_final: 0.2556 (mmt-90) REVERT: C 355 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8281 (mm-30) REVERT: C 435 ARG cc_start: 0.7854 (mtp-110) cc_final: 0.7530 (ttm110) REVERT: D 69 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8199 (mp0) REVERT: D 100 ASP cc_start: 0.9031 (t0) cc_final: 0.8570 (t70) REVERT: D 186 GLN cc_start: 0.9042 (tp-100) cc_final: 0.8801 (tp-100) REVERT: D 334 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8875 (mt0) REVERT: E 42 LEU cc_start: 0.8921 (tp) cc_final: 0.8524 (tp) REVERT: E 80 LEU cc_start: 0.8808 (mt) cc_final: 0.8529 (mt) REVERT: F 44 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7427 (mp10) REVERT: H 7 LEU cc_start: 0.9420 (tp) cc_final: 0.9099 (tt) REVERT: H 17 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7586 (mm-30) REVERT: H 31 MET cc_start: 0.9016 (ttp) cc_final: 0.8771 (ttm) REVERT: L 7 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6688 (mtp85) REVERT: L 8 GLN cc_start: 0.8701 (mm-40) cc_final: 0.7976 (mt0) REVERT: T 1 MET cc_start: 0.7121 (tpp) cc_final: 0.6361 (tpp) REVERT: y 27 MET cc_start: 0.8532 (tmm) cc_final: 0.8011 (ptt) REVERT: 2 23 LEU cc_start: 0.7983 (tm) cc_final: 0.7668 (pp) REVERT: 2 25 ARG cc_start: 0.7384 (tpp80) cc_final: 0.7149 (ttt90) REVERT: 2 35 MET cc_start: 0.8022 (mpp) cc_final: 0.7674 (mpp) REVERT: 2 43 ILE cc_start: 0.8764 (tp) cc_final: 0.8464 (tt) REVERT: 2 56 MET cc_start: 0.8912 (mtm) cc_final: 0.8703 (mtm) REVERT: 2 60 GLU cc_start: 0.7690 (tt0) cc_final: 0.7102 (pp20) REVERT: 2 71 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8260 (tppp) REVERT: 2 94 ARG cc_start: 0.7543 (tpm170) cc_final: 0.6972 (tpm170) REVERT: 2 96 ILE cc_start: 0.8493 (mm) cc_final: 0.8224 (mm) REVERT: 2 99 MET cc_start: 0.8861 (tpt) cc_final: 0.8426 (tmt) REVERT: 2 100 ASP cc_start: 0.9077 (m-30) cc_final: 0.8775 (p0) REVERT: 2 111 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7176 (pp30) REVERT: 3 7 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5757 (pm20) REVERT: 3 10 ARG cc_start: 0.6836 (mpt90) cc_final: 0.6521 (mpt90) outliers start: 57 outliers final: 42 residues processed: 523 average time/residue: 0.4947 time to fit residues: 301.5903 Evaluate side-chains 530 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 482 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 334 GLN Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 7 ARG Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 49 LEU Chi-restraints excluded: chain 2 residue 68 VAL Chi-restraints excluded: chain 2 residue 71 LYS Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 7 GLU Chi-restraints excluded: chain 3 residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 118 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 189 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 0.0050 chunk 8 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 HIS D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN 2 45 GLN 2 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.131851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097450 restraints weight = 34302.718| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.63 r_work: 0.3016 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.908 21814 Z= 0.132 Angle : 0.715 14.395 30089 Z= 0.336 Chirality : 0.043 0.348 2914 Planarity : 0.005 0.047 3788 Dihedral : 14.134 87.865 3455 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.31 % Allowed : 28.75 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.19), residues: 2203 helix: 1.67 (0.15), residues: 1227 sheet: -0.38 (0.62), residues: 75 loop : -0.31 (0.22), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 476 TYR 0.026 0.001 TYR C 328 PHE 0.027 0.001 PHE A 274 TRP 0.075 0.001 TRP K 39 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (21795) covalent geometry : angle 0.71486 / 0.34 (30089) hydrogen bonds : bond 0.04207 / 2.85 ( 970) hydrogen bonds : angle 4.10907 / 3.03 ( 2796) Misc. bond : bond 0.20828 / 9.92 ( 19) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7762.28 seconds wall clock time: 132 minutes 33.14 seconds (7953.14 seconds total)