Starting phenix.real_space_refine on Thu Mar 5 13:27:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nhq_12337/03_2026/7nhq_12337.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nhq_12337/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7nhq_12337/03_2026/7nhq_12337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nhq_12337/03_2026/7nhq_12337.map" model { file = "/net/cci-nas-00/data/ceres_data/7nhq_12337/03_2026/7nhq_12337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nhq_12337/03_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-5986/lib/python3.9/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: 4.11, per 1000 atoms: 0.20 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: 1.80 Conformation dependent library (CDL) restraints added in 799.4 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: 0.55 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: 3.22 Time building geometry restraints manager: 2.25 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: 29050 5.48 - 10.96: 794 10.96 - 16.45: 212 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: 10714 26.07 - 52.14: 670 52.14 - 78.21: 138 78.21 - 104.28: 72 104.28 - 130.35: 17 Dihedral angle restraints: 11611 sinusoidal: 5288 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 11608 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: 3782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO D 406 " -0.085 2.00e-02 2.50e+03 1.81e-01 2.62e+03 pdb=" ND PHO D 406 " -0.294 2.00e-02 2.50e+03 pdb=" C1A PHO D 406 " -0.114 2.00e-02 2.50e+03 pdb=" C1B PHO D 406 " 0.021 2.00e-02 2.50e+03 pdb=" C1C PHO D 406 " -0.177 2.00e-02 2.50e+03 pdb=" C1D PHO D 406 " -0.175 2.00e-02 2.50e+03 pdb=" C2A PHO D 406 " 0.106 2.00e-02 2.50e+03 pdb=" C2B PHO D 406 " 0.015 2.00e-02 2.50e+03 pdb=" C2C PHO D 406 " 0.038 2.00e-02 2.50e+03 pdb=" C2D PHO D 406 " -0.067 2.00e-02 2.50e+03 pdb=" C3A PHO D 406 " 0.343 2.00e-02 2.50e+03 pdb=" C3B PHO D 406 " -0.062 2.00e-02 2.50e+03 pdb=" C3C PHO D 406 " 0.146 2.00e-02 2.50e+03 pdb=" C3D PHO D 406 " -0.105 2.00e-02 2.50e+03 pdb=" C4A PHO D 406 " 0.112 2.00e-02 2.50e+03 pdb=" C4B PHO D 406 " -0.135 2.00e-02 2.50e+03 pdb=" C4C PHO D 406 " -0.093 2.00e-02 2.50e+03 pdb=" C4D PHO D 406 " -0.198 2.00e-02 2.50e+03 pdb=" CAB PHO D 406 " -0.055 2.00e-02 2.50e+03 pdb=" CAC PHO D 406 " 0.464 2.00e-02 2.50e+03 pdb=" CAD PHO D 406 " 0.078 2.00e-02 2.50e+03 pdb=" CBD PHO D 406 " -0.093 2.00e-02 2.50e+03 pdb=" CHA PHO D 406 " -0.175 2.00e-02 2.50e+03 pdb=" CHB PHO D 406 " 0.153 2.00e-02 2.50e+03 pdb=" CHC PHO D 406 " -0.106 2.00e-02 2.50e+03 pdb=" CHD PHO D 406 " -0.077 2.00e-02 2.50e+03 pdb=" CMB PHO D 406 " 0.169 2.00e-02 2.50e+03 pdb=" CMC PHO D 406 " 0.256 2.00e-02 2.50e+03 pdb=" CMD PHO D 406 " 0.095 2.00e-02 2.50e+03 pdb=" NA PHO D 406 " -0.067 2.00e-02 2.50e+03 pdb=" NC PHO D 406 " -0.287 2.00e-02 2.50e+03 pdb=" OBD PHO D 406 " 0.371 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO A 404 " -0.030 2.00e-02 2.50e+03 1.26e-01 1.27e+03 pdb=" ND PHO A 404 " 0.086 2.00e-02 2.50e+03 pdb=" C1A PHO A 404 " 0.068 2.00e-02 2.50e+03 pdb=" C1B PHO A 404 " -0.064 2.00e-02 2.50e+03 pdb=" C1C PHO A 404 " 0.047 2.00e-02 2.50e+03 pdb=" C1D PHO A 404 " 0.015 2.00e-02 2.50e+03 pdb=" C2A PHO A 404 " -0.041 2.00e-02 2.50e+03 pdb=" C2B PHO A 404 " 0.065 2.00e-02 2.50e+03 pdb=" C2C PHO A 404 " -0.038 2.00e-02 2.50e+03 pdb=" C2D PHO A 404 " -0.024 2.00e-02 2.50e+03 pdb=" C3A PHO A 404 " -0.393 2.00e-02 2.50e+03 pdb=" C3B PHO A 404 " 0.137 2.00e-02 2.50e+03 pdb=" C3C PHO A 404 " -0.074 2.00e-02 2.50e+03 pdb=" C3D PHO A 404 " 0.104 2.00e-02 2.50e+03 pdb=" C4A PHO A 404 " -0.195 2.00e-02 2.50e+03 pdb=" C4B PHO A 404 " 0.072 2.00e-02 2.50e+03 pdb=" C4C PHO A 404 " 0.012 2.00e-02 2.50e+03 pdb=" C4D PHO A 404 " 0.132 2.00e-02 2.50e+03 pdb=" CAB PHO A 404 " 0.197 2.00e-02 2.50e+03 pdb=" CAC PHO A 404 " -0.167 2.00e-02 2.50e+03 pdb=" CAD PHO A 404 " 0.077 2.00e-02 2.50e+03 pdb=" CBD PHO A 404 " 0.202 2.00e-02 2.50e+03 pdb=" CHA PHO A 404 " 0.153 2.00e-02 2.50e+03 pdb=" CHB PHO A 404 " -0.199 2.00e-02 2.50e+03 pdb=" CHC PHO A 404 " 0.054 2.00e-02 2.50e+03 pdb=" CHD PHO A 404 " -0.009 2.00e-02 2.50e+03 pdb=" CMB PHO A 404 " 0.064 2.00e-02 2.50e+03 pdb=" CMC PHO A 404 " -0.127 2.00e-02 2.50e+03 pdb=" CMD PHO A 404 " -0.145 2.00e-02 2.50e+03 pdb=" NA PHO A 404 " -0.051 2.00e-02 2.50e+03 pdb=" NC PHO A 404 " 0.082 2.00e-02 2.50e+03 pdb=" OBD PHO A 404 " -0.009 2.00e-02 2.50e+03 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 ... (remaining 3779 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.620 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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= 1.712 Angle : 2.313 27.411 30089 Z= 0.977 Chirality : 0.414 4.420 2914 Planarity : 0.017 0.181 3782 Dihedral : 19.571 130.346 7577 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 covalent geometry : bond 0.01223 (21795) covalent geometry : angle 2.31300 (30089) hydrogen bonds : bond 0.16815 ( 970) hydrogen bonds : angle 6.48755 ( 2796) Misc. bond : bond 0.57229 ( 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 : 0.666 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: 0.4908 time to fit residues: 457.4644 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 : 1.004 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 F 41 GLN H 15 ASN Z 6 GLN 2 45 GLN 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 = 0.140407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106310 restraints weight = 34024.349| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.68 r_work: 0.3167 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 1.740 21814 Z= 1.193 Angle : 0.934 18.804 30089 Z= 0.408 Chirality : 0.064 0.736 2914 Planarity : 0.007 0.050 3782 Dihedral : 18.858 120.178 3778 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.59 % Favored : 97.23 % Rotamer: Outliers : 4.36 % Allowed : 20.03 % Favored : 75.61 % 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: -0.73 (0.17), residues: 2203 helix: 0.24 (0.14), residues: 1239 sheet: 0.07 (0.63), residues: 54 loop : -1.49 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 127 TYR 0.019 0.002 TYR B 279 PHE 0.026 0.002 PHE B 246 TRP 0.044 0.002 TRP 2 92 HIS 0.010 0.002 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00393 (21795) covalent geometry : angle 0.93442 (30089) hydrogen bonds : bond 0.06545 ( 970) hydrogen bonds : angle 4.94296 ( 2796) Misc. bond : bond 0.43949 ( 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 673 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 594 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.9190 (t80) cc_final: 0.8761 (t80) REVERT: A 65 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7610 (mm-30) REVERT: A 142 TRP cc_start: 0.8187 (m-10) cc_final: 0.7575 (m-10) REVERT: A 187 GLN cc_start: 0.9323 (tp40) cc_final: 0.8934 (tp40) REVERT: A 257 ARG cc_start: 0.7235 (tpt90) cc_final: 0.6988 (tpt90) REVERT: B 130 GLU cc_start: 0.8634 (mp0) cc_final: 0.8421 (mp0) REVERT: B 281 GLN cc_start: 0.8881 (tt0) cc_final: 0.8457 (tt0) REVERT: B 313 ASP cc_start: 0.9303 (t0) cc_final: 0.9041 (t0) REVERT: B 378 LYS cc_start: 0.9035 (mttp) cc_final: 0.8785 (mttp) REVERT: C 71 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8231 (mt-10) REVERT: C 141 ASP cc_start: 0.8787 (t0) cc_final: 0.8506 (t0) REVERT: C 193 ASP cc_start: 0.8211 (t0) cc_final: 0.7758 (t0) REVERT: C 350 ARG cc_start: 0.5375 (pmt170) cc_final: 0.2914 (mmt-90) REVERT: C 409 SER cc_start: 0.8911 (t) cc_final: 0.8704 (p) REVERT: D 42 TYR cc_start: 0.9203 (t80) cc_final: 0.8992 (t80) REVERT: D 100 ASP cc_start: 0.8809 (t0) cc_final: 0.8283 (t0) REVERT: D 105 CYS cc_start: 0.9369 (m) cc_final: 0.9044 (m) REVERT: D 210 LEU cc_start: 0.9010 (mt) cc_final: 0.8782 (mt) REVERT: D 246 MET cc_start: 0.8916 (tpt) cc_final: 0.8624 (tpt) REVERT: D 263 ASN cc_start: 0.8558 (t0) cc_final: 0.8226 (t0) REVERT: D 297 ASP cc_start: 0.9261 (p0) cc_final: 0.9052 (p0) REVERT: D 318 ASN cc_start: 0.9294 (m-40) cc_final: 0.8991 (m110) REVERT: E 62 SER cc_start: 0.8923 (m) cc_final: 0.8566 (p) REVERT: H 3 ARG cc_start: 0.8420 (ptm160) cc_final: 0.8147 (ptm-80) REVERT: H 50 ASN cc_start: 0.9103 (t0) cc_final: 0.8829 (t0) REVERT: K 18 PHE cc_start: 0.8077 (m-10) cc_final: 0.7793 (m-10) REVERT: L 7 ARG cc_start: 0.6962 (tmt170) cc_final: 0.6508 (tmt-80) REVERT: L 8 GLN cc_start: 0.8711 (mm110) cc_final: 0.8246 (mm110) REVERT: L 11 GLU cc_start: 0.8412 (pt0) cc_final: 0.8174 (pt0) REVERT: M 5 GLN cc_start: 0.7262 (mm-40) cc_final: 0.6738 (pm20) REVERT: T 1 MET cc_start: 0.6798 (tpp) cc_final: 0.6032 (tpp) REVERT: X 8 LYS cc_start: 0.8487 (mtpp) cc_final: 0.7954 (mtpp) REVERT: X 12 ILE cc_start: 0.9136 (mt) cc_final: 0.8890 (mp) REVERT: Z 37 LYS cc_start: 0.6134 (ttmt) cc_final: 0.5846 (ttmm) REVERT: 2 23 LEU cc_start: 0.8584 (tt) cc_final: 0.8084 (mt) REVERT: 2 35 MET cc_start: 0.7529 (mpp) cc_final: 0.7218 (mpp) REVERT: 2 45 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8123 (pt0) REVERT: 2 73 ILE cc_start: 0.9248 (mm) cc_final: 0.8936 (mm) REVERT: 2 83 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7786 (p) REVERT: 2 96 ILE cc_start: 0.8509 (mt) cc_final: 0.8113 (mm) REVERT: 2 99 MET cc_start: 0.8834 (tpt) cc_final: 0.8299 (tmm) REVERT: 2 100 ASP cc_start: 0.9095 (m-30) cc_final: 0.8680 (m-30) outliers start: 79 outliers final: 32 residues processed: 626 average time/residue: 0.4789 time to fit residues: 348.7440 Evaluate side-chains 576 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 542 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 207 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 260 SER 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 156 LEU 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 F residue 23 VAL 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 21 ILE Chi-restraints excluded: chain X residue 34 ILE 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 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: 0.9980 chunk 43 optimal weight: 1.9990 chunk 196 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 150 optimal weight: 0.0270 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN B 157 HIS B 338 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102366 restraints weight = 34152.581| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.62 r_work: 0.3102 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.870 21814 Z= 0.168 Angle : 0.780 14.391 30089 Z= 0.351 Chirality : 0.053 0.633 2914 Planarity : 0.005 0.047 3782 Dihedral : 17.242 119.979 3755 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 5.52 % Allowed : 20.97 % Favored : 73.51 % 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: 0.18 (0.18), residues: 2203 helix: 1.00 (0.15), residues: 1234 sheet: 0.34 (0.65), residues: 54 loop : -1.10 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 2 25 TYR 0.019 0.001 TYR H 49 PHE 0.024 0.001 PHE B 246 TRP 0.020 0.001 TRP C 211 HIS 0.006 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00368 (21795) covalent geometry : angle 0.78038 (30089) hydrogen bonds : bond 0.05439 ( 970) hydrogen bonds : angle 4.48949 ( 2796) Misc. bond : bond 0.19982 ( 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 653 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 553 time to evaluate : 0.640 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: 0.8019 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 132 GLU cc_start: 0.8952 (tt0) cc_final: 0.8587 (tt0) REVERT: A 142 TRP cc_start: 0.8147 (m-10) cc_final: 0.7726 (m-10) REVERT: A 187 GLN cc_start: 0.9299 (tp40) cc_final: 0.9077 (tm-30) REVERT: A 225 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8329 (ptp-170) REVERT: A 296 ASN cc_start: 0.9047 (m-40) cc_final: 0.8747 (t0) REVERT: B 130 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: B 214 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8733 (mm) REVERT: B 313 ASP cc_start: 0.9285 (t0) cc_final: 0.9055 (t0) REVERT: B 349 LYS cc_start: 0.9144 (tmmm) cc_final: 0.8628 (mttp) REVERT: B 378 LYS cc_start: 0.9080 (mttp) cc_final: 0.8650 (mttp) REVERT: C 71 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8301 (mt-10) REVERT: C 141 ASP cc_start: 0.8695 (t0) cc_final: 0.8252 (t0) REVERT: C 183 ASP cc_start: 0.8160 (t0) cc_final: 0.7861 (t0) REVERT: C 193 ASP cc_start: 0.8232 (t0) cc_final: 0.7784 (t0) REVERT: C 285 TYR cc_start: 0.9129 (m-80) cc_final: 0.8926 (m-80) REVERT: C 409 SER cc_start: 0.8854 (t) cc_final: 0.8561 (p) REVERT: C 435 ARG cc_start: 0.7908 (mtp-110) cc_final: 0.7684 (ttm110) REVERT: D 42 TYR cc_start: 0.9236 (t80) cc_final: 0.8991 (t80) REVERT: D 100 ASP cc_start: 0.8921 (t0) cc_final: 0.8372 (t0) REVERT: D 105 CYS cc_start: 0.9402 (m) cc_final: 0.9156 (m) REVERT: D 186 GLN cc_start: 0.9338 (tp40) cc_final: 0.9022 (tp-100) REVERT: D 210 LEU cc_start: 0.9028 (mt) cc_final: 0.8809 (mt) REVERT: D 246 MET cc_start: 0.8973 (tpt) cc_final: 0.8664 (tpt) REVERT: D 297 ASP cc_start: 0.9207 (p0) cc_final: 0.8988 (p0) REVERT: D 301 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8612 (mm-40) REVERT: E 62 SER cc_start: 0.9008 (m) cc_final: 0.8621 (p) REVERT: E 80 LEU cc_start: 0.8863 (mt) cc_final: 0.8453 (mt) REVERT: F 44 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7178 (mp10) REVERT: H 17 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8171 (mm-30) REVERT: I 5 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8089 (tttp) REVERT: K 18 PHE cc_start: 0.8193 (m-10) cc_final: 0.7892 (m-10) REVERT: T 1 MET cc_start: 0.6814 (tpp) cc_final: 0.6088 (tpp) REVERT: X 8 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8045 (mtpp) REVERT: X 12 ILE cc_start: 0.9183 (mt) cc_final: 0.8915 (mp) REVERT: Z 6 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8028 (mt0) REVERT: Z 29 SER cc_start: 0.8493 (t) cc_final: 0.8022 (p) REVERT: Z 34 ASP cc_start: 0.9038 (m-30) cc_final: 0.8789 (m-30) REVERT: 2 4 MET cc_start: 0.1211 (pmm) cc_final: 0.0099 (ptt) REVERT: 2 23 LEU cc_start: 0.8465 (tt) cc_final: 0.8113 (mt) REVERT: 2 35 MET cc_start: 0.7722 (mpp) cc_final: 0.7365 (mpp) REVERT: 2 43 ILE cc_start: 0.8556 (tp) cc_final: 0.8298 (tt) REVERT: 2 83 THR cc_start: 0.8331 (m) cc_final: 0.8014 (p) REVERT: 2 99 MET cc_start: 0.8887 (tpt) cc_final: 0.8377 (tmm) REVERT: 2 100 ASP cc_start: 0.9190 (m-30) cc_final: 0.8985 (m-30) REVERT: 2 111 GLN cc_start: 0.7551 (tm-30) cc_final: 0.7072 (tm-30) REVERT: 3 24 GLN cc_start: 0.8193 (pm20) cc_final: 0.7945 (mp10) outliers start: 100 outliers final: 38 residues processed: 595 average time/residue: 0.4987 time to fit residues: 344.7619 Evaluate side-chains 560 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 515 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 222 SER Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 214 LEU 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 273 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 342 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 301 GLN Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 17 GLU 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 28 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain T residue 3 THR 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 68 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 58 optimal weight: 0.0670 chunk 183 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.093979 restraints weight = 34291.253| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.59 r_work: 0.2970 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.609 21814 Z= 0.234 Angle : 0.810 14.790 30089 Z= 0.365 Chirality : 0.053 0.470 2914 Planarity : 0.006 0.060 3782 Dihedral : 16.936 120.798 3755 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 6.51 % Allowed : 21.36 % Favored : 72.13 % 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: 0.46 (0.18), residues: 2203 helix: 1.18 (0.15), residues: 1233 sheet: -0.63 (0.63), residues: 58 loop : -0.80 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 46 TYR 0.022 0.002 TYR C 328 PHE 0.026 0.002 PHE X 10 TRP 0.023 0.002 TRP Z 33 HIS 0.009 0.002 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00527 (21795) covalent geometry : angle 0.80968 (30089) hydrogen bonds : bond 0.05943 ( 970) hydrogen bonds : angle 4.45969 ( 2796) Misc. bond : bond 0.14115 ( 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 644 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 526 time to evaluate : 0.778 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: 0.8207 (mm-30) cc_final: 0.7962 (mm-30) REVERT: A 136 ARG cc_start: 0.8817 (tpp-160) cc_final: 0.8310 (tpp-160) REVERT: A 142 TRP cc_start: 0.8198 (m-10) cc_final: 0.7722 (m-10) REVERT: A 187 GLN cc_start: 0.9352 (tp40) cc_final: 0.9093 (tm-30) REVERT: B 214 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8929 (mm) REVERT: B 313 ASP cc_start: 0.9294 (t0) cc_final: 0.9062 (t0) REVERT: B 349 LYS cc_start: 0.9190 (tmmm) cc_final: 0.8917 (mttp) REVERT: B 378 LYS cc_start: 0.9101 (mttp) cc_final: 0.8774 (mttp) REVERT: C 50 PHE cc_start: 0.9479 (t80) cc_final: 0.9267 (t80) REVERT: C 115 PHE cc_start: 0.9036 (t80) cc_final: 0.8699 (t80) REVERT: C 141 ASP cc_start: 0.8632 (t0) cc_final: 0.8029 (t0) REVERT: C 183 ASP cc_start: 0.8417 (t0) cc_final: 0.7987 (t0) REVERT: C 193 ASP cc_start: 0.8282 (t0) cc_final: 0.7777 (t0) REVERT: C 342 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: C 350 ARG cc_start: 0.6062 (pmt170) cc_final: 0.2845 (mmt-90) REVERT: C 384 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.9006 (tmm) REVERT: C 435 ARG cc_start: 0.7974 (mtp-110) cc_final: 0.7674 (ttm110) REVERT: D 42 TYR cc_start: 0.9328 (t80) cc_final: 0.9046 (t80) REVERT: D 100 ASP cc_start: 0.9071 (t0) cc_final: 0.8617 (t70) REVERT: D 295 SER cc_start: 0.9364 (p) cc_final: 0.9153 (p) REVERT: D 297 ASP cc_start: 0.9277 (p0) cc_final: 0.9049 (p0) REVERT: E 62 SER cc_start: 0.9082 (m) cc_final: 0.8685 (p) REVERT: E 71 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8081 (mm-30) REVERT: E 80 LEU cc_start: 0.8817 (mt) cc_final: 0.8482 (mt) REVERT: F 44 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7308 (mp10) REVERT: H 3 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8553 (ptp-170) REVERT: H 4 ARG cc_start: 0.9216 (mmm-85) cc_final: 0.8965 (mmm-85) REVERT: H 17 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7977 (mm-30) REVERT: I 5 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8077 (ttpp) REVERT: K 18 PHE cc_start: 0.8214 (m-10) cc_final: 0.7884 (m-10) REVERT: L 7 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6782 (tmt-80) REVERT: L 8 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8224 (mp10) REVERT: M 8 LEU cc_start: 0.8993 (tm) cc_final: 0.8781 (tp) REVERT: T 1 MET cc_start: 0.7140 (tpp) cc_final: 0.6348 (tpp) REVERT: T 24 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8068 (ptt-90) REVERT: X 8 LYS cc_start: 0.8550 (mtpp) cc_final: 0.8119 (mtpp) REVERT: X 12 ILE cc_start: 0.9211 (mt) cc_final: 0.8957 (mp) REVERT: Z 6 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8028 (mp10) REVERT: 2 4 MET cc_start: 0.1777 (pmm) cc_final: 0.1299 (ptt) REVERT: 2 15 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7842 (mm-30) REVERT: 2 23 LEU cc_start: 0.8497 (tt) cc_final: 0.8154 (pp) REVERT: 2 35 MET cc_start: 0.7844 (mpp) cc_final: 0.7380 (mpp) REVERT: 2 43 ILE cc_start: 0.8652 (tp) cc_final: 0.8287 (tt) REVERT: 2 60 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6341 (mt-10) REVERT: 2 83 THR cc_start: 0.8479 (m) cc_final: 0.8107 (p) REVERT: 2 96 ILE cc_start: 0.8542 (mm) cc_final: 0.8255 (mm) REVERT: 2 99 MET cc_start: 0.8891 (tpt) cc_final: 0.8452 (tmm) REVERT: 2 100 ASP cc_start: 0.9186 (m-30) cc_final: 0.8969 (m-30) REVERT: 2 101 ARG cc_start: 0.8194 (mtt90) cc_final: 0.7636 (mtt90) REVERT: 2 111 GLN cc_start: 0.7774 (tm-30) cc_final: 0.7086 (tm-30) REVERT: 3 24 GLN cc_start: 0.8115 (pm20) cc_final: 0.7900 (mp10) outliers start: 118 outliers final: 56 residues processed: 589 average time/residue: 0.4986 time to fit residues: 341.6946 Evaluate side-chains 560 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 495 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 157 VAL Chi-restraints excluded: chain A residue 222 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 333 GLU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 148 LEU 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 373 LYS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 72 GLN 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 215 VAL 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 C residue 342 GLU Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain D residue 17 ILE 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 F residue 28 VAL Chi-restraints excluded: chain H residue 3 ARG 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 I residue 5 LYS Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 7 ARG Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 SER 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 5 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 33 TRP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 66 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 201 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 403 ASN D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN K 40 GLN 2 45 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.129812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.094685 restraints weight = 34150.975| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.63 r_work: 0.2994 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.598 21814 Z= 0.166 Angle : 0.716 14.587 30089 Z= 0.329 Chirality : 0.048 0.385 2914 Planarity : 0.005 0.042 3782 Dihedral : 16.476 120.064 3755 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.08 % Allowed : 24.34 % Favored : 70.58 % 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: 0.79 (0.18), residues: 2203 helix: 1.41 (0.15), residues: 1235 sheet: 0.37 (0.69), residues: 48 loop : -0.66 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 476 TYR 0.033 0.001 TYR C 328 PHE 0.024 0.001 PHE X 10 TRP 0.022 0.001 TRP Z 33 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00372 (21795) covalent geometry : angle 0.71604 (30089) hydrogen bonds : bond 0.05137 ( 970) hydrogen bonds : angle 4.27205 ( 2796) Misc. bond : bond 0.13799 ( 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 623 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 531 time to evaluate : 0.656 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: 0.8268 (mm-30) cc_final: 0.7997 (mm-30) REVERT: A 142 TRP cc_start: 0.8214 (m-10) cc_final: 0.7621 (m-10) REVERT: A 187 GLN cc_start: 0.9336 (tp40) cc_final: 0.9132 (tm-30) REVERT: A 307 ILE cc_start: 0.9096 (pt) cc_final: 0.8798 (pp) REVERT: B 130 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8564 (mp0) REVERT: B 350 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8490 (tm-30) REVERT: B 378 LYS cc_start: 0.9116 (mttp) cc_final: 0.8641 (mttm) REVERT: C 141 ASP cc_start: 0.8523 (t0) cc_final: 0.7931 (t0) REVERT: C 183 ASP cc_start: 0.8506 (t0) cc_final: 0.7978 (t0) REVERT: C 193 ASP cc_start: 0.8262 (t0) cc_final: 0.7758 (t0) REVERT: C 350 ARG cc_start: 0.5991 (pmt170) cc_final: 0.2670 (mmt-90) REVERT: C 371 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8323 (t70) REVERT: D 100 ASP cc_start: 0.9028 (t0) cc_final: 0.8500 (t0) REVERT: D 244 TYR cc_start: 0.9543 (p90) cc_final: 0.9227 (p90) REVERT: D 307 GLU cc_start: 0.7469 (pp20) cc_final: 0.7251 (pp20) REVERT: E 62 SER cc_start: 0.9093 (m) cc_final: 0.8675 (p) REVERT: E 71 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8285 (mm-30) REVERT: E 74 GLN cc_start: 0.7731 (pm20) cc_final: 0.7527 (pm20) REVERT: E 77 GLU cc_start: 0.8897 (tp30) cc_final: 0.8684 (tp30) REVERT: E 80 LEU cc_start: 0.8796 (mt) cc_final: 0.8431 (mt) REVERT: F 44 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7343 (mp10) REVERT: H 3 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8460 (ptp-170) REVERT: H 4 ARG cc_start: 0.9223 (mmm-85) cc_final: 0.8970 (mmm-85) REVERT: H 17 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7971 (mm-30) REVERT: K 18 PHE cc_start: 0.8210 (m-10) cc_final: 0.7911 (m-10) REVERT: L 7 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6811 (tmt-80) REVERT: L 8 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8169 (mp10) REVERT: M 30 GLU cc_start: 0.7563 (pp20) cc_final: 0.7124 (OUTLIER) REVERT: T 1 MET cc_start: 0.7148 (tpp) cc_final: 0.6583 (tpp) REVERT: T 5 THR cc_start: 0.8952 (m) cc_final: 0.8673 (p) REVERT: T 24 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8050 (ptt-90) REVERT: X 8 LYS cc_start: 0.8562 (mtpp) cc_final: 0.8132 (mtpp) REVERT: X 12 ILE cc_start: 0.9212 (mt) cc_final: 0.8962 (mp) REVERT: Z 6 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8130 (mt0) REVERT: Z 17 PHE cc_start: 0.8872 (t80) cc_final: 0.8621 (t80) REVERT: 2 4 MET cc_start: 0.1794 (pmm) cc_final: 0.1309 (ptt) REVERT: 2 15 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7327 (tp30) REVERT: 2 23 LEU cc_start: 0.8442 (tt) cc_final: 0.8139 (pp) REVERT: 2 35 MET cc_start: 0.7993 (mpp) cc_final: 0.7623 (mpp) REVERT: 2 43 ILE cc_start: 0.8660 (tp) cc_final: 0.8281 (tt) REVERT: 2 60 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7072 (tm-30) REVERT: 2 71 LYS cc_start: 0.8700 (tppp) cc_final: 0.8470 (tppp) REVERT: 2 83 THR cc_start: 0.8550 (m) cc_final: 0.8173 (p) REVERT: 2 96 ILE cc_start: 0.8502 (mm) cc_final: 0.8201 (mm) REVERT: 2 99 MET cc_start: 0.8871 (tpt) cc_final: 0.8400 (tmt) REVERT: 2 100 ASP cc_start: 0.9203 (m-30) cc_final: 0.8993 (m-30) REVERT: 2 111 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7077 (tm-30) REVERT: 3 7 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5597 (pm20) REVERT: 3 24 GLN cc_start: 0.8170 (pm20) cc_final: 0.7669 (mp10) outliers start: 92 outliers final: 43 residues processed: 573 average time/residue: 0.5050 time to fit residues: 334.7113 Evaluate side-chains 552 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 502 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 157 VAL Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 175 THR 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 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 230 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 78 VAL 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 286 VAL 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 3 ARG Chi-restraints excluded: chain H residue 10 ILE 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 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 6 GLN Chi-restraints excluded: chain Z residue 46 LEU Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 2 residue 68 VAL Chi-restraints excluded: chain 3 residue 7 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 99 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 68 optimal weight: 0.1980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN C 62 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN 2 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.094867 restraints weight = 34202.400| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.64 r_work: 0.2999 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.538 21814 Z= 0.151 Angle : 0.698 14.554 30089 Z= 0.323 Chirality : 0.046 0.300 2914 Planarity : 0.005 0.043 3782 Dihedral : 16.046 119.601 3752 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.02 % Allowed : 25.06 % Favored : 69.92 % 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: 0.99 (0.18), residues: 2203 helix: 1.57 (0.15), residues: 1233 sheet: 0.48 (0.72), residues: 48 loop : -0.56 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 476 TYR 0.042 0.001 TYR C 328 PHE 0.026 0.001 PHE X 10 TRP 0.029 0.001 TRP Z 33 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00340 (21795) covalent geometry : angle 0.69766 (30089) hydrogen bonds : bond 0.04918 ( 970) hydrogen bonds : angle 4.18319 ( 2796) Misc. bond : bond 0.12431 ( 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 619 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 528 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.9315 (t80) cc_final: 0.8541 (t80) REVERT: A 65 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7978 (mm-30) REVERT: A 142 TRP cc_start: 0.8138 (m-10) cc_final: 0.7397 (m-10) REVERT: A 307 ILE cc_start: 0.9073 (pt) cc_final: 0.8762 (pp) REVERT: B 119 ASP cc_start: 0.8670 (p0) cc_final: 0.8454 (p0) REVERT: B 378 LYS cc_start: 0.9090 (mttp) cc_final: 0.8751 (mttp) REVERT: C 141 ASP cc_start: 0.8529 (t0) cc_final: 0.7869 (t0) REVERT: C 183 ASP cc_start: 0.8538 (t0) cc_final: 0.8319 (t0) REVERT: C 193 ASP cc_start: 0.8315 (t0) cc_final: 0.7822 (t0) REVERT: C 277 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8707 (t80) REVERT: C 350 ARG cc_start: 0.6030 (pmt170) cc_final: 0.2662 (mmt-90) REVERT: C 355 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8262 (mm-30) REVERT: C 435 ARG cc_start: 0.8128 (ttm110) cc_final: 0.7903 (ttm110) REVERT: C 437 ARG cc_start: 0.7639 (mmm160) cc_final: 0.7267 (mmm160) REVERT: D 36 LEU cc_start: 0.9547 (tp) cc_final: 0.9310 (tp) REVERT: D 100 ASP cc_start: 0.9035 (t0) cc_final: 0.8585 (t70) REVERT: D 244 TYR cc_start: 0.9554 (p90) cc_final: 0.9234 (p90) REVERT: D 334 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8904 (mt0) REVERT: E 62 SER cc_start: 0.9085 (m) cc_final: 0.8633 (p) REVERT: E 71 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8212 (mm-30) REVERT: E 77 GLU cc_start: 0.8957 (tp30) cc_final: 0.8611 (mt-10) REVERT: E 80 LEU cc_start: 0.8830 (mt) cc_final: 0.8564 (mt) REVERT: F 44 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7469 (mp10) REVERT: H 3 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8470 (ptp-170) REVERT: H 4 ARG cc_start: 0.9277 (mmm-85) cc_final: 0.9034 (mmm-85) REVERT: H 17 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7890 (mm-30) REVERT: L 7 ARG cc_start: 0.7475 (tmt170) cc_final: 0.6815 (tmt-80) REVERT: L 8 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8189 (mp10) REVERT: M 30 GLU cc_start: 0.7621 (pp20) cc_final: 0.7269 (pp20) REVERT: T 1 MET cc_start: 0.7351 (tpp) cc_final: 0.6674 (tpp) REVERT: T 5 THR cc_start: 0.8873 (m) cc_final: 0.8635 (p) REVERT: X 8 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8139 (mtpp) REVERT: X 36 LYS cc_start: 0.6520 (pmtt) cc_final: 0.6172 (pptt) REVERT: Z 6 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8119 (mt0) REVERT: 2 15 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7348 (tp30) REVERT: 2 35 MET cc_start: 0.8033 (mpp) cc_final: 0.7603 (mpp) REVERT: 2 43 ILE cc_start: 0.8659 (tp) cc_final: 0.8266 (tt) REVERT: 2 96 ILE cc_start: 0.8462 (mm) cc_final: 0.8152 (mm) REVERT: 2 99 MET cc_start: 0.8886 (tpt) cc_final: 0.8436 (tmt) REVERT: 2 100 ASP cc_start: 0.9173 (m-30) cc_final: 0.8958 (m-30) REVERT: 2 111 GLN cc_start: 0.7819 (tm-30) cc_final: 0.6927 (pp30) REVERT: 3 7 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5597 (pm20) outliers start: 91 outliers final: 57 residues processed: 570 average time/residue: 0.5019 time to fit residues: 331.8998 Evaluate side-chains 572 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 509 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 137 LEU 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 239 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 175 THR 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 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 252 PHE Chi-restraints excluded: chain C residue 269 MET 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 17 ILE Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 132 ILE 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 301 GLN Chi-restraints excluded: chain D residue 334 GLN Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 3 ARG 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 33 SER Chi-restraints excluded: chain M residue 20 VAL 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 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 5 THR Chi-restraints excluded: chain 3 residue 7 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 113 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 386 HIS C 403 ASN D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN K 40 GLN Z 58 ASN 2 45 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.096008 restraints weight = 34099.124| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.64 r_work: 0.2992 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.549 21814 Z= 0.136 Angle : 0.697 13.700 30089 Z= 0.324 Chirality : 0.044 0.274 2914 Planarity : 0.004 0.043 3782 Dihedral : 15.705 119.263 3752 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.69 % Allowed : 26.10 % Favored : 69.21 % 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: 1.13 (0.18), residues: 2203 helix: 1.70 (0.15), residues: 1225 sheet: 0.60 (0.74), residues: 48 loop : -0.50 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 476 TYR 0.037 0.001 TYR C 328 PHE 0.025 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 covalent geometry : bond 0.00302 (21795) covalent geometry : angle 0.69723 (30089) hydrogen bonds : bond 0.04596 ( 970) hydrogen bonds : angle 4.12455 ( 2796) Misc. bond : bond 0.12629 ( 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 594 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 509 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.9268 (t80) cc_final: 0.8720 (t80) REVERT: A 65 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7791 (mm-30) REVERT: B 119 ASP cc_start: 0.8674 (p0) cc_final: 0.8421 (p0) REVERT: B 130 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8438 (mp0) REVERT: B 409 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8116 (mm-40) REVERT: C 74 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8056 (mm) REVERT: C 183 ASP cc_start: 0.8562 (t0) cc_final: 0.8317 (t0) REVERT: C 193 ASP cc_start: 0.8293 (t0) cc_final: 0.7808 (t0) REVERT: C 350 ARG cc_start: 0.5870 (pmt170) cc_final: 0.2507 (mmt-90) REVERT: C 437 ARG cc_start: 0.7595 (mmm160) cc_final: 0.7230 (mmm160) REVERT: D 100 ASP cc_start: 0.9004 (t0) cc_final: 0.8532 (t70) REVERT: D 244 TYR cc_start: 0.9536 (p90) cc_final: 0.9258 (p90) REVERT: D 334 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8887 (mt0) REVERT: E 62 SER cc_start: 0.9081 (m) cc_final: 0.8614 (p) REVERT: E 77 GLU cc_start: 0.8949 (tp30) cc_final: 0.8739 (tp30) REVERT: E 80 LEU cc_start: 0.8814 (mt) cc_final: 0.8497 (mt) REVERT: F 44 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7428 (mp10) REVERT: H 3 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8434 (ptp-170) REVERT: H 4 ARG cc_start: 0.9275 (mmm-85) cc_final: 0.9015 (mmm-85) REVERT: H 7 LEU cc_start: 0.9420 (tp) cc_final: 0.9111 (tt) REVERT: H 17 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7768 (mm-30) REVERT: I 9 TYR cc_start: 0.8790 (m-10) cc_final: 0.8548 (m-80) REVERT: L 4 ASN cc_start: 0.8569 (t0) cc_final: 0.8368 (t0) REVERT: L 7 ARG cc_start: 0.7437 (tmt170) cc_final: 0.6825 (tmt-80) REVERT: L 8 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8178 (mp10) REVERT: M 30 GLU cc_start: 0.7631 (pp20) cc_final: 0.7292 (pp20) REVERT: T 1 MET cc_start: 0.7367 (tpp) cc_final: 0.6731 (tpp) REVERT: T 24 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8240 (ptm-80) REVERT: X 36 LYS cc_start: 0.6490 (pmtt) cc_final: 0.6157 (pptt) REVERT: y 27 MET cc_start: 0.8512 (tmm) cc_final: 0.8110 (ptt) REVERT: Z 6 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: Z 34 ASP cc_start: 0.8849 (m-30) cc_final: 0.8627 (m-30) REVERT: Z 46 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8792 (tt) REVERT: 2 15 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7219 (tp30) REVERT: 2 35 MET cc_start: 0.7986 (mpp) cc_final: 0.7578 (mpp) REVERT: 2 43 ILE cc_start: 0.8630 (tp) cc_final: 0.8225 (tt) REVERT: 2 60 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7418 (pp20) REVERT: 2 94 ARG cc_start: 0.7660 (tpm170) cc_final: 0.7091 (tpm170) REVERT: 2 96 ILE cc_start: 0.8482 (mm) cc_final: 0.8158 (mm) REVERT: 2 99 MET cc_start: 0.8902 (tpt) cc_final: 0.8422 (tmt) REVERT: 2 100 ASP cc_start: 0.9202 (m-30) cc_final: 0.8999 (m-30) REVERT: 2 111 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7402 (tm-30) REVERT: 3 7 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5574 (pm20) REVERT: 3 10 ARG cc_start: 0.6790 (mpt90) cc_final: 0.6502 (mpt90) REVERT: 3 22 GLN cc_start: 0.8280 (tp40) cc_final: 0.8064 (tp40) outliers start: 85 outliers final: 45 residues processed: 554 average time/residue: 0.5006 time to fit residues: 321.2232 Evaluate side-chains 544 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 489 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 291 SER 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 240 ILE Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain D residue 17 ILE 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 286 VAL Chi-restraints excluded: chain D residue 334 GLN 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 3 ARG 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 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 20 VAL Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain Z residue 46 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 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: 0.8980 chunk 45 optimal weight: 0.0470 chunk 3 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 123 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN Z 58 ASN ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094936 restraints weight = 33958.103| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.60 r_work: 0.2977 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.536 21814 Z= 0.151 Angle : 0.705 13.955 30089 Z= 0.329 Chirality : 0.045 0.254 2914 Planarity : 0.004 0.042 3782 Dihedral : 15.456 119.343 3752 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.53 % Allowed : 27.04 % Favored : 68.43 % 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: 1.12 (0.18), residues: 2203 helix: 1.69 (0.15), residues: 1216 sheet: 0.08 (0.66), residues: 65 loop : -0.47 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 476 TYR 0.034 0.001 TYR C 328 PHE 0.025 0.001 PHE A 274 TRP 0.046 0.001 TRP Z 33 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00343 (21795) covalent geometry : angle 0.70470 (30089) hydrogen bonds : bond 0.04735 ( 970) hydrogen bonds : angle 4.11790 ( 2796) Misc. bond : bond 0.12347 ( 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 586 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 504 time to evaluate : 0.693 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: 0.9243 (t80) cc_final: 0.8655 (t80) REVERT: A 64 ARG cc_start: 0.7956 (mmm-85) cc_final: 0.7740 (mmm-85) REVERT: A 65 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7853 (mm-30) REVERT: A 127 MET cc_start: 0.9083 (ttm) cc_final: 0.8850 (ttp) REVERT: A 142 TRP cc_start: 0.8139 (m-10) cc_final: 0.7299 (m-10) REVERT: A 307 ILE cc_start: 0.9069 (pt) cc_final: 0.8748 (pp) REVERT: A 333 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8038 (tm-30) REVERT: B 119 ASP cc_start: 0.8679 (p0) cc_final: 0.8396 (p0) REVERT: B 409 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8129 (mm-40) REVERT: C 71 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8566 (mt-10) REVERT: C 193 ASP cc_start: 0.8314 (t0) cc_final: 0.7831 (t0) REVERT: C 350 ARG cc_start: 0.5847 (pmt170) cc_final: 0.2466 (mmt-90) REVERT: C 355 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8198 (mm-30) REVERT: C 437 ARG cc_start: 0.7614 (mmm160) cc_final: 0.7248 (mmm160) REVERT: D 100 ASP cc_start: 0.9027 (t0) cc_final: 0.8558 (t70) REVERT: D 244 TYR cc_start: 0.9543 (p90) cc_final: 0.9262 (p90) REVERT: D 265 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8446 (ttp80) REVERT: D 334 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8867 (mt0) REVERT: E 62 SER cc_start: 0.9104 (m) cc_final: 0.8636 (p) REVERT: E 77 GLU cc_start: 0.8947 (tp30) cc_final: 0.8739 (tp30) REVERT: E 80 LEU cc_start: 0.8787 (mt) cc_final: 0.8474 (mt) REVERT: F 44 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7449 (mp10) REVERT: H 3 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8468 (ptp-170) REVERT: H 4 ARG cc_start: 0.9267 (mmm-85) cc_final: 0.9001 (mmm-85) REVERT: H 17 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7636 (mm-30) REVERT: I 9 TYR cc_start: 0.8762 (m-10) cc_final: 0.8530 (m-80) REVERT: L 7 ARG cc_start: 0.7525 (tmt170) cc_final: 0.6849 (mtp85) REVERT: L 8 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8085 (mp10) REVERT: M 30 GLU cc_start: 0.7670 (pp20) cc_final: 0.7316 (pp20) REVERT: T 1 MET cc_start: 0.7630 (tpp) cc_final: 0.6892 (tpp) REVERT: X 8 LYS cc_start: 0.8429 (mtpp) cc_final: 0.8192 (mtmt) REVERT: X 36 LYS cc_start: 0.6526 (pmtt) cc_final: 0.6263 (pptt) REVERT: y 27 MET cc_start: 0.8512 (tmm) cc_final: 0.8169 (ptt) REVERT: Z 6 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8149 (mt0) REVERT: Z 46 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8770 (tt) REVERT: 2 15 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7307 (tp30) REVERT: 2 35 MET cc_start: 0.8034 (mpp) cc_final: 0.7593 (mpp) REVERT: 2 43 ILE cc_start: 0.8640 (tp) cc_final: 0.8236 (tt) REVERT: 2 60 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7452 (pp20) REVERT: 2 94 ARG cc_start: 0.7620 (tpm170) cc_final: 0.7183 (tpm170) REVERT: 2 96 ILE cc_start: 0.8469 (mm) cc_final: 0.8152 (mm) REVERT: 2 99 MET cc_start: 0.8905 (tpt) cc_final: 0.8432 (tmt) REVERT: 2 100 ASP cc_start: 0.9189 (m-30) cc_final: 0.8973 (m-30) REVERT: 2 111 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7470 (tm-30) REVERT: 3 7 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.5533 (pm20) REVERT: 3 10 ARG cc_start: 0.6844 (mpt90) cc_final: 0.6515 (mpt90) outliers start: 82 outliers final: 52 residues processed: 541 average time/residue: 0.5286 time to fit residues: 330.8148 Evaluate side-chains 552 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 493 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL 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 242 GLU 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 130 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 291 SER 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 240 ILE Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain D residue 17 ILE 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 286 VAL 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 3 ARG Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 55 LEU 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 6 LEU Chi-restraints excluded: chain M residue 20 VAL 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 39 LEU Chi-restraints excluded: chain Z residue 46 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 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: 0.8980 chunk 203 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 7 optimal weight: 0.0060 chunk 168 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 HIS D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.131097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096398 restraints weight = 33829.724| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.63 r_work: 0.3003 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.535 21814 Z= 0.131 Angle : 0.696 14.248 30089 Z= 0.325 Chirality : 0.044 0.323 2914 Planarity : 0.004 0.044 3782 Dihedral : 15.201 119.335 3752 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.81 % Allowed : 27.54 % Favored : 68.65 % 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: 1.71 (0.15), residues: 1219 sheet: 0.57 (0.69), residues: 60 loop : -0.42 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 476 TYR 0.031 0.001 TYR C 328 PHE 0.027 0.001 PHE A 274 TRP 0.043 0.001 TRP Z 33 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00295 (21795) covalent geometry : angle 0.69564 (30089) hydrogen bonds : bond 0.04404 ( 970) hydrogen bonds : angle 4.08178 ( 2796) Misc. bond : bond 0.12286 ( 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 572 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 503 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.9246 (t80) cc_final: 0.8804 (t80) REVERT: A 65 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7817 (mm-30) REVERT: A 127 MET cc_start: 0.9057 (ttm) cc_final: 0.8838 (ttp) REVERT: A 142 TRP cc_start: 0.8097 (m-10) cc_final: 0.7167 (m-10) REVERT: A 307 ILE cc_start: 0.9060 (pt) cc_final: 0.8724 (pp) REVERT: A 326 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8721 (tp) REVERT: A 333 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8014 (tm-30) REVERT: A 335 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.7137 (m110) REVERT: B 119 ASP cc_start: 0.8662 (p0) cc_final: 0.8376 (p0) REVERT: B 130 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8434 (mp0) REVERT: B 409 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8135 (mm-40) REVERT: B 492 GLU cc_start: 0.7958 (mp0) cc_final: 0.7193 (pp20) REVERT: C 50 PHE cc_start: 0.9398 (t80) cc_final: 0.9160 (t80) REVERT: C 71 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8600 (mt-10) REVERT: C 193 ASP cc_start: 0.8307 (t0) cc_final: 0.7817 (t0) REVERT: C 350 ARG cc_start: 0.5823 (pmt170) cc_final: 0.2429 (mmt-90) REVERT: C 355 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8291 (mm-30) REVERT: D 100 ASP cc_start: 0.9012 (t0) cc_final: 0.8548 (t70) REVERT: D 244 TYR cc_start: 0.9523 (p90) cc_final: 0.9212 (p90) REVERT: D 265 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8438 (ttp80) REVERT: D 334 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8832 (mt0) REVERT: E 62 SER cc_start: 0.9114 (m) cc_final: 0.8669 (p) REVERT: E 77 GLU cc_start: 0.8965 (tp30) cc_final: 0.8758 (tp30) REVERT: E 80 LEU cc_start: 0.8800 (mt) cc_final: 0.8521 (mt) REVERT: F 44 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7439 (mp10) REVERT: H 3 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8592 (ptp-170) REVERT: H 4 ARG cc_start: 0.9258 (mmm-85) cc_final: 0.8992 (mmm-85) REVERT: H 7 LEU cc_start: 0.9416 (tp) cc_final: 0.9098 (tt) REVERT: H 15 ASN cc_start: 0.9382 (t0) cc_final: 0.9175 (t0) REVERT: H 17 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7591 (mm-30) REVERT: I 9 TYR cc_start: 0.8727 (m-10) cc_final: 0.8497 (m-80) REVERT: L 7 ARG cc_start: 0.7591 (tmt170) cc_final: 0.6838 (tmt-80) REVERT: M 30 GLU cc_start: 0.7668 (pp20) cc_final: 0.7354 (pp20) REVERT: T 1 MET cc_start: 0.7351 (tpp) cc_final: 0.6647 (tpp) REVERT: X 8 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8078 (mtmt) REVERT: y 27 MET cc_start: 0.8507 (tmm) cc_final: 0.8164 (ptt) REVERT: Z 46 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8762 (tt) REVERT: 2 35 MET cc_start: 0.8040 (mpp) cc_final: 0.7595 (mpp) REVERT: 2 43 ILE cc_start: 0.8601 (tp) cc_final: 0.8162 (tt) REVERT: 2 60 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7296 (pp20) REVERT: 2 94 ARG cc_start: 0.7551 (tpm170) cc_final: 0.7146 (tpm170) REVERT: 2 96 ILE cc_start: 0.8444 (mm) cc_final: 0.8119 (mm) REVERT: 2 99 MET cc_start: 0.8889 (tpt) cc_final: 0.8379 (tmt) REVERT: 2 100 ASP cc_start: 0.9184 (m-30) cc_final: 0.8936 (m-30) REVERT: 2 111 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7450 (tm-30) REVERT: 3 2 ARG cc_start: 0.5521 (OUTLIER) cc_final: 0.5076 (mmp80) REVERT: 3 7 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5507 (pm20) outliers start: 69 outliers final: 45 residues processed: 537 average time/residue: 0.5160 time to fit residues: 320.2011 Evaluate side-chains 536 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 481 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 242 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 291 SER 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 B residue 442 ILE 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 240 ILE Chi-restraints excluded: chain C residue 269 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 262 SER Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 286 VAL 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 3 ARG 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 2 GLU 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 Z residue 39 LEU Chi-restraints excluded: chain Z residue 46 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 2 ARG 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: 6.9990 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 106 optimal weight: 7.9990 chunk 209 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 HIS D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN y 21 GLN ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096190 restraints weight = 34123.132| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.62 r_work: 0.2999 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.526 21814 Z= 0.135 Angle : 0.697 14.778 30089 Z= 0.328 Chirality : 0.044 0.344 2914 Planarity : 0.004 0.043 3782 Dihedral : 15.059 119.084 3750 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.37 % Allowed : 28.70 % 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: 1.18 (0.18), residues: 2203 helix: 1.65 (0.15), residues: 1224 sheet: 0.59 (0.69), residues: 60 loop : -0.34 (0.22), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 476 TYR 0.030 0.001 TYR C 328 PHE 0.027 0.001 PHE A 274 TRP 0.053 0.001 TRP Z 33 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00305 (21795) covalent geometry : angle 0.69691 (30089) hydrogen bonds : bond 0.04411 ( 970) hydrogen bonds : angle 4.09912 ( 2796) Misc. bond : bond 0.12075 ( 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 549 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 488 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.9212 (t80) cc_final: 0.8504 (t80) REVERT: A 64 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7786 (mmm-85) REVERT: A 65 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7804 (mm-30) REVERT: A 136 ARG cc_start: 0.8701 (tpp-160) cc_final: 0.8309 (tpp-160) REVERT: A 142 TRP cc_start: 0.8173 (m-10) cc_final: 0.7269 (m-10) REVERT: A 307 ILE cc_start: 0.9133 (pt) cc_final: 0.8805 (pp) REVERT: A 326 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8698 (tp) REVERT: A 329 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8256 (tm-30) REVERT: B 119 ASP cc_start: 0.8670 (p0) cc_final: 0.8378 (p0) REVERT: B 130 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8585 (mp0) REVERT: B 409 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8146 (mm-40) REVERT: B 492 GLU cc_start: 0.7882 (mp0) cc_final: 0.7293 (pp20) REVERT: C 59 GLU cc_start: 0.8925 (tp30) cc_final: 0.8644 (tm-30) REVERT: C 193 ASP cc_start: 0.8321 (t0) cc_final: 0.7830 (t0) REVERT: C 350 ARG cc_start: 0.5806 (pmt170) cc_final: 0.2435 (mmt-90) REVERT: C 355 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8286 (mm-30) REVERT: C 382 GLU cc_start: 0.8903 (pp20) cc_final: 0.8588 (tm-30) REVERT: D 69 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8259 (mp0) REVERT: D 100 ASP cc_start: 0.9034 (t0) cc_final: 0.8496 (t0) REVERT: D 244 TYR cc_start: 0.9534 (p90) cc_final: 0.9223 (p90) REVERT: D 265 ARG cc_start: 0.8653 (ttp80) cc_final: 0.8453 (ttp80) REVERT: D 334 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8839 (mt0) REVERT: E 62 SER cc_start: 0.9119 (m) cc_final: 0.8678 (p) REVERT: E 80 LEU cc_start: 0.8795 (mt) cc_final: 0.8502 (mt) REVERT: F 44 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7439 (mp10) REVERT: H 3 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8485 (ptp-170) REVERT: H 4 ARG cc_start: 0.9264 (mmm-85) cc_final: 0.9020 (mmm-85) REVERT: H 7 LEU cc_start: 0.9422 (tp) cc_final: 0.9108 (tt) REVERT: H 17 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: I 9 TYR cc_start: 0.8721 (m-10) cc_final: 0.8505 (m-80) REVERT: L 1 MET cc_start: 0.6676 (ppp) cc_final: 0.6062 (pp-130) REVERT: L 7 ARG cc_start: 0.7568 (tmt170) cc_final: 0.6741 (mtp85) REVERT: L 8 GLN cc_start: 0.8641 (mm-40) cc_final: 0.7921 (mt0) REVERT: M 30 GLU cc_start: 0.7697 (pp20) cc_final: 0.7377 (pp20) REVERT: T 1 MET cc_start: 0.7301 (tpp) cc_final: 0.6532 (tpp) REVERT: y 27 MET cc_start: 0.8443 (tmm) cc_final: 0.8166 (ptt) REVERT: Z 46 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8759 (tt) REVERT: 2 35 MET cc_start: 0.8091 (mpp) cc_final: 0.7680 (mpp) REVERT: 2 43 ILE cc_start: 0.8529 (tp) cc_final: 0.8210 (tt) REVERT: 2 60 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7284 (pp20) REVERT: 2 94 ARG cc_start: 0.7524 (tpm170) cc_final: 0.7224 (tpm170) REVERT: 2 96 ILE cc_start: 0.8453 (mm) cc_final: 0.8194 (mm) REVERT: 2 99 MET cc_start: 0.8897 (tpt) cc_final: 0.8474 (tmt) REVERT: 2 100 ASP cc_start: 0.9149 (m-30) cc_final: 0.8816 (p0) REVERT: 2 111 GLN cc_start: 0.7744 (tm-30) cc_final: 0.7412 (tm-30) REVERT: 3 2 ARG cc_start: 0.5594 (OUTLIER) cc_final: 0.5134 (mmp80) REVERT: 3 7 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5410 (pm20) outliers start: 61 outliers final: 37 residues processed: 518 average time/residue: 0.5209 time to fit residues: 312.2674 Evaluate side-chains 527 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 481 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 242 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 148 LEU 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 112 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 269 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 262 SER Chi-restraints excluded: chain D residue 286 VAL 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 3 ARG 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 33 SER Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain Z residue 46 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 2 ARG 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: 6.9990 chunk 60 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 189 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 45 optimal weight: 0.0010 chunk 3 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097393 restraints weight = 34121.728| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.62 r_work: 0.3019 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.522 21814 Z= 0.127 Angle : 0.689 15.063 30089 Z= 0.325 Chirality : 0.043 0.353 2914 Planarity : 0.004 0.044 3782 Dihedral : 14.848 119.553 3750 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.15 % Allowed : 29.14 % Favored : 67.72 % 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: 1.21 (0.19), residues: 2203 helix: 1.68 (0.15), residues: 1224 sheet: -0.12 (0.65), residues: 70 loop : -0.27 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 476 TYR 0.030 0.001 TYR C 328 PHE 0.028 0.001 PHE A 274 TRP 0.063 0.001 TRP K 39 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00283 (21795) covalent geometry : angle 0.68875 (30089) hydrogen bonds : bond 0.04164 ( 970) hydrogen bonds : angle 4.05770 ( 2796) Misc. bond : bond 0.11986 ( 19) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8496.76 seconds wall clock time: 144 minutes 38.94 seconds (8678.94 seconds total)