Starting phenix.real_space_refine on Wed Mar 4 13:30:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cq7_30438/03_2026/7cq7_30438.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cq7_30438/03_2026/7cq7_30438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cq7_30438/03_2026/7cq7_30438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cq7_30438/03_2026/7cq7_30438.map" model { file = "/net/cci-nas-00/data/ceres_data/7cq7_30438/03_2026/7cq7_30438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cq7_30438/03_2026/7cq7_30438.cif" } resolution = 3.55 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 92 5.16 5 Cl 3 4.86 5 C 8926 2.51 5 N 2304 2.21 5 O 2481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 13810 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1630 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1637 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5194 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 28, 'TRANS': 647} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 5236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5236 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CL': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CL': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.11, per 1000 atoms: 0.23 Number of scatterers: 13810 At special positions: 0 Unit cell: (136.14, 111.986, 132.846, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 92 16.00 P 4 15.00 O 2481 8.00 N 2304 7.00 C 8926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 115 " distance=2.03 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 174 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 255 " distance=2.04 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 438 " - pdb=" SG CYS D 454 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG E 1 " - " ASN A 263 " " NAG F 1 " - " ASN B 263 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 509.5 milliseconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3312 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 10 sheets defined 63.9% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 81 through 105 removed outlier: 3.783A pdb=" N GLU A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.750A pdb=" N GLN A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 183 through 203 removed outlier: 3.684A pdb=" N ASN A 203 " --> pdb=" O CYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.923A pdb=" N CYS A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 217 through 222' Processing helix chain 'A' and resid 224 through 245 removed outlier: 3.813A pdb=" N TYR A 228 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 Processing helix chain 'A' and resid 281 through 294 removed outlier: 4.260A pdb=" N VAL A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 306 Processing helix chain 'B' and resid 81 through 105 removed outlier: 4.311A pdb=" N GLU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N PHE B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 130 removed outlier: 3.710A pdb=" N ILE B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.983A pdb=" N ALA B 149 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP B 150 " --> pdb=" O LEU B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 150' Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 185 through 203 removed outlier: 3.586A pdb=" N ASN B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.841A pdb=" N CYS B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 217 through 222' Processing helix chain 'B' and resid 224 through 246 removed outlier: 4.223A pdb=" N THR B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 removed outlier: 3.540A pdb=" N ALA B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 removed outlier: 3.625A pdb=" N VAL B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 306 Proline residue: B 296 - end of helix removed outlier: 3.610A pdb=" N SER B 303 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 122 through 167 removed outlier: 3.596A pdb=" N ARG C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 159 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 196 removed outlier: 4.301A pdb=" N SER C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 removed outlier: 3.863A pdb=" N CYS C 211 " --> pdb=" O PRO C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.682A pdb=" N ILE C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 250 through 263 removed outlier: 3.956A pdb=" N GLN C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 removed outlier: 3.879A pdb=" N ARG C 280 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 302 removed outlier: 3.698A pdb=" N ARG C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 312 removed outlier: 3.734A pdb=" N VAL C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 346 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 374 through 407 removed outlier: 3.749A pdb=" N ALA C 380 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG C 405 " --> pdb=" O MET C 401 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR C 406 " --> pdb=" O PHE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 434 removed outlier: 3.805A pdb=" N ALA C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 469 through 480 removed outlier: 3.549A pdb=" N SER C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 504 removed outlier: 4.084A pdb=" N PHE C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 531 removed outlier: 3.647A pdb=" N LEU C 527 " --> pdb=" O ALA C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 536 Processing helix chain 'C' and resid 543 through 560 removed outlier: 3.890A pdb=" N LEU C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 573 Processing helix chain 'C' and resid 576 through 578 No H-bonds generated for 'chain 'C' and resid 576 through 578' Processing helix chain 'C' and resid 579 through 596 removed outlier: 3.783A pdb=" N VAL C 596 " --> pdb=" O ILE C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 608 Processing helix chain 'C' and resid 645 through 652 Processing helix chain 'C' and resid 681 through 690 removed outlier: 3.628A pdb=" N HIS C 690 " --> pdb=" O VAL C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 713 removed outlier: 3.720A pdb=" N ASP C 713 " --> pdb=" O ASP C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 724 Processing helix chain 'C' and resid 753 through 763 removed outlier: 3.838A pdb=" N LYS C 759 " --> pdb=" O PRO C 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.706A pdb=" N ARG D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 166 removed outlier: 3.618A pdb=" N LYS D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP D 164 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 196 removed outlier: 3.673A pdb=" N LEU D 178 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 removed outlier: 3.565A pdb=" N ALA D 202 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.547A pdb=" N ASN D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 239 Processing helix chain 'D' and resid 248 through 262 removed outlier: 4.423A pdb=" N HIS D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 302 Processing helix chain 'D' and resid 303 through 314 Processing helix chain 'D' and resid 320 through 346 removed outlier: 3.915A pdb=" N HIS D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 374 through 406 removed outlier: 4.230A pdb=" N ALA D 390 " --> pdb=" O GLY D 386 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 434 removed outlier: 3.644A pdb=" N ALA D 417 " --> pdb=" O GLN D 413 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 418 " --> pdb=" O VAL D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 466 Processing helix chain 'D' and resid 469 through 478 removed outlier: 3.601A pdb=" N SER D 473 " --> pdb=" O THR D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 504 removed outlier: 4.601A pdb=" N PHE D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 536 removed outlier: 3.509A pdb=" N ALA D 523 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY D 529 " --> pdb=" O GLY D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 560 removed outlier: 3.608A pdb=" N TYR D 547 " --> pdb=" O ASP D 543 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET D 550 " --> pdb=" O LYS D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 574 removed outlier: 4.004A pdb=" N THR D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 578 No H-bonds generated for 'chain 'D' and resid 576 through 578' Processing helix chain 'D' and resid 579 through 596 Processing helix chain 'D' and resid 600 through 608 Processing helix chain 'D' and resid 646 through 652 removed outlier: 3.596A pdb=" N SER D 652 " --> pdb=" O VAL D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 685 Processing helix chain 'D' and resid 685 through 690 Processing helix chain 'D' and resid 753 through 762 removed outlier: 3.902A pdb=" N LYS D 759 " --> pdb=" O PRO D 755 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 265 through 266 Processing sheet with id=AA2, first strand: chain 'C' and resid 438 through 440 Processing sheet with id=AA3, first strand: chain 'C' and resid 638 through 639 Processing sheet with id=AA4, first strand: chain 'C' and resid 642 through 643 removed outlier: 4.231A pdb=" N GLU C 642 " --> pdb=" O MET C 735 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET C 735 " --> pdb=" O GLU C 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 747 through 748 removed outlier: 5.691A pdb=" N VAL C 748 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU C 769 " --> pdb=" O LEU C 781 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU C 781 " --> pdb=" O LEU C 769 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL C 771 " --> pdb=" O VAL C 779 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.946A pdb=" N GLU D 95 " --> pdb=" O LYS D 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 438 through 439 Processing sheet with id=AA8, first strand: chain 'D' and resid 638 through 639 removed outlier: 3.714A pdb=" N GLY D 677 " --> pdb=" O VAL D 663 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 641 through 643 removed outlier: 3.632A pdb=" N GLU D 642 " --> pdb=" O MET D 735 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 747 through 749 removed outlier: 6.471A pdb=" N VAL D 748 " --> pdb=" O VAL D 772 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 758 hydrogen bonds defined for protein. 2235 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4350 1.34 - 1.47: 3464 1.47 - 1.59: 6154 1.59 - 1.71: 6 1.71 - 1.83: 140 Bond restraints: 14114 Sorted by residual: bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C5 ADP D 901 " pdb=" C6 ADP D 901 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 ADP C 901 " pdb=" C6 ADP C 901 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" CB VAL C 586 " pdb=" CG1 VAL C 586 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.49e+00 ... (remaining 14109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 18276 2.18 - 4.36: 742 4.36 - 6.54: 109 6.54 - 8.72: 43 8.72 - 10.90: 15 Bond angle restraints: 19185 Sorted by residual: angle pdb=" C THR A 282 " pdb=" N VAL A 283 " pdb=" CA VAL A 283 " ideal model delta sigma weight residual 120.24 125.32 -5.08 6.30e-01 2.52e+00 6.50e+01 angle pdb=" N GLN D 722 " pdb=" CA GLN D 722 " pdb=" C GLN D 722 " ideal model delta sigma weight residual 114.75 105.85 8.90 1.26e+00 6.30e-01 4.99e+01 angle pdb=" C ARG B 271 " pdb=" N THR B 272 " pdb=" CA THR B 272 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C ARG A 271 " pdb=" N THR A 272 " pdb=" CA THR A 272 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.49e+01 angle pdb=" N ILE D 724 " pdb=" CA ILE D 724 " pdb=" C ILE D 724 " ideal model delta sigma weight residual 110.62 115.92 -5.30 1.14e+00 7.69e-01 2.16e+01 ... (remaining 19180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 8213 22.84 - 45.68: 182 45.68 - 68.52: 10 68.52 - 91.36: 8 91.36 - 114.20: 1 Dihedral angle restraints: 8414 sinusoidal: 3299 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASP C 282 " pdb=" C ASP C 282 " pdb=" N THR C 283 " pdb=" CA THR C 283 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" C5' ADP D 901 " pdb=" O5' ADP D 901 " pdb=" PA ADP D 901 " pdb=" O2A ADP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 -174.20 114.20 1 2.00e+01 2.50e-03 3.38e+01 dihedral pdb=" CA ARG A 107 " pdb=" C ARG A 107 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " ideal model delta harmonic sigma weight residual 180.00 152.58 27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 8411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1658 0.060 - 0.120: 513 0.120 - 0.180: 68 0.180 - 0.240: 11 0.240 - 0.301: 2 Chirality restraints: 2252 Sorted by residual: chirality pdb=" CB ILE D 721 " pdb=" CA ILE D 721 " pdb=" CG1 ILE D 721 " pdb=" CG2 ILE D 721 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE C 724 " pdb=" CA ILE C 724 " pdb=" CG1 ILE C 724 " pdb=" CG2 ILE C 724 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB ILE D 275 " pdb=" CA ILE D 275 " pdb=" CG1 ILE D 275 " pdb=" CG2 ILE D 275 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2249 not shown) Planarity restraints: 2399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 179 " 0.028 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP C 179 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP C 179 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 179 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 179 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 179 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 179 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 179 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 179 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 179 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 783 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C THR C 783 " 0.048 2.00e-02 2.50e+03 pdb=" O THR C 783 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG C 784 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 349 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C MET D 349 " -0.044 2.00e-02 2.50e+03 pdb=" O MET D 349 " 0.016 2.00e-02 2.50e+03 pdb=" N TRP D 350 " 0.015 2.00e-02 2.50e+03 ... (remaining 2396 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 75 2.51 - 3.11: 10133 3.11 - 3.71: 21215 3.71 - 4.30: 29202 4.30 - 4.90: 49468 Nonbonded interactions: 110093 Sorted by model distance: nonbonded pdb=" OD2 ASP D 786 " pdb=" O2' ADP D 901 " model vdw 1.915 3.040 nonbonded pdb=" O MET C 368 " pdb=" OH TYR C 579 " model vdw 2.236 3.040 nonbonded pdb=" CG HIS C 658 " pdb=" N7 ADP C 901 " model vdw 2.251 2.672 nonbonded pdb=" O MET D 368 " pdb=" OH TYR D 579 " model vdw 2.261 3.040 nonbonded pdb=" NH2 ARG D 767 " pdb=" O2B ADP D 901 " model vdw 2.261 3.120 ... (remaining 110088 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 73 through 306) selection = (chain 'B' and (resid 73 through 130 or resid 142 through 245 or resid 253 throu \ gh 306)) } ncs_group { reference = (chain 'C' and (resid 94 through 115 or (resid 116 and (name N or name CA or nam \ e C or name O or name CB )) or resid 121 through 652 or (resid 653 through 656 a \ nd (name N or name CA or name C or name O or name CB )) or resid 657 through 664 \ or resid 673 through 693 or resid 706 through 789 or (resid 790 and (name N or \ name CA or name C or name O or name CB )) or resid 901 through 902)) selection = (chain 'D' and (resid 94 through 116 or resid 121 through 366 or (resid 367 and \ (name N or name CA or name C or name O or name CB )) or resid 368 through 619 or \ (resid 620 and (name N or name CA or name C or name O or name CB )) or resid 62 \ 1 through 642 or (resid 643 and (name N or name CA or name C or name O or name C \ B )) or resid 644 through 690 or (resid 691 and (name N or name CA or name C or \ name O or name CB )) or resid 692 or (resid 693 and (name N or name CA or name C \ or name O or name CB )) or resid 706 through 707 or (resid 708 and (name N or n \ ame CA or name C or name O or name CB )) or resid 709 through 716 or (resid 717 \ and (name N or name CA or name C or name O or name CB )) or resid 718 or (resid \ 719 and (name N or name CA or name C or name O or name CB )) or resid 720 throug \ h 724 or (resid 725 through 732 and (name N or name CA or name C or name O or na \ me CB )) or resid 733 through 902)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue 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: 1.400 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.420 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4342 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 : 0.010 0.641 14135 Z= 0.697 Angle : 1.074 10.899 19221 Z= 0.571 Chirality : 0.056 0.301 2252 Planarity : 0.008 0.063 2397 Dihedral : 10.352 114.200 5066 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -4.47 (0.15), residues: 1734 helix: -2.46 (0.12), residues: 1046 sheet: None (None), residues: 0 loop : -3.68 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 326 TYR 0.022 0.002 TYR D 370 PHE 0.031 0.003 PHE D 279 TRP 0.062 0.004 TRP C 179 HIS 0.020 0.002 HIS D 725 Details of bonding type rmsd covalent geometry : bond 0.00804 (14114) covalent geometry : angle 1.06949 (19185) SS BOND : bond 0.00331 ( 12) SS BOND : angle 1.82474 ( 24) hydrogen bonds : bond 0.20482 ( 758) hydrogen bonds : angle 7.64867 ( 2235) Misc. bond : bond 0.32045 ( 5) link_BETA1-4 : bond 0.00595 ( 2) link_BETA1-4 : angle 2.74501 ( 6) link_NAG-ASN : bond 0.00305 ( 2) link_NAG-ASN : angle 3.75561 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 468 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 VAL cc_start: 0.5320 (t) cc_final: 0.4733 (m) REVERT: C 588 MET cc_start: 0.4373 (mtp) cc_final: 0.4140 (ppp) REVERT: D 227 LEU cc_start: 0.6605 (tp) cc_final: 0.6105 (tt) REVERT: D 275 ILE cc_start: 0.5375 (tp) cc_final: 0.5134 (mp) REVERT: D 513 VAL cc_start: 0.7961 (p) cc_final: 0.7596 (p) outliers start: 1 outliers final: 0 residues processed: 469 average time/residue: 0.1193 time to fit residues: 80.4064 Evaluate side-chains 250 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0470 chunk 149 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN A 202 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 173 ASN C 183 ASN C 220 HIS C 774 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS D 396 ASN D 623 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.129502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.113797 restraints weight = 31608.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.116924 restraints weight = 14577.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.118932 restraints weight = 8338.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.120161 restraints weight = 5544.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.121137 restraints weight = 4193.033| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5085 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14135 Z= 0.170 Angle : 0.839 13.542 19221 Z= 0.416 Chirality : 0.045 0.287 2252 Planarity : 0.006 0.051 2397 Dihedral : 6.795 108.783 1996 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.09 % Allowed : 11.34 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.38 (0.19), residues: 1734 helix: -0.44 (0.15), residues: 1068 sheet: None (None), residues: 0 loop : -3.54 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 526 TYR 0.019 0.002 TYR C 547 PHE 0.035 0.002 PHE A 294 TRP 0.029 0.002 TRP D 179 HIS 0.010 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00362 (14114) covalent geometry : angle 0.83333 (19185) SS BOND : bond 0.00805 ( 12) SS BOND : angle 2.19005 ( 24) hydrogen bonds : bond 0.05006 ( 758) hydrogen bonds : angle 4.68435 ( 2235) Misc. bond : bond 0.00451 ( 5) link_BETA1-4 : bond 0.00812 ( 2) link_BETA1-4 : angle 1.64949 ( 6) link_NAG-ASN : bond 0.00702 ( 2) link_NAG-ASN : angle 3.76955 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 291 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7270 (tpp) cc_final: 0.5583 (tpp) REVERT: A 168 GLU cc_start: 0.6463 (tm-30) cc_final: 0.6104 (tm-30) REVERT: A 304 PHE cc_start: 0.7199 (t80) cc_final: 0.6993 (t80) REVERT: B 192 LEU cc_start: 0.8460 (tp) cc_final: 0.7775 (mp) REVERT: B 255 CYS cc_start: 0.3216 (OUTLIER) cc_final: 0.2628 (t) REVERT: B 281 ASP cc_start: 0.6888 (p0) cc_final: 0.6614 (p0) REVERT: C 323 LEU cc_start: 0.4751 (OUTLIER) cc_final: 0.3790 (mt) REVERT: C 433 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.6295 (t80) REVERT: C 570 MET cc_start: 0.5592 (mmp) cc_final: 0.5335 (mmp) REVERT: C 588 MET cc_start: 0.5619 (mtp) cc_final: 0.4832 (ppp) REVERT: C 599 GLU cc_start: 0.4533 (OUTLIER) cc_final: 0.3319 (pm20) REVERT: C 659 ASN cc_start: 0.3933 (m-40) cc_final: 0.3011 (m110) REVERT: D 132 LEU cc_start: 0.7600 (mt) cc_final: 0.7383 (mt) REVERT: D 143 PHE cc_start: 0.7602 (t80) cc_final: 0.5910 (m-10) REVERT: D 368 MET cc_start: 0.6275 (mtt) cc_final: 0.5403 (mpp) REVERT: D 598 ILE cc_start: 0.7912 (mm) cc_final: 0.7671 (mm) outliers start: 46 outliers final: 20 residues processed: 319 average time/residue: 0.0954 time to fit residues: 47.4610 Evaluate side-chains 248 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 433 TYR Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 517 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain D residue 787 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 0.0570 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN B 113 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN D 479 HIS D 623 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.128438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.112523 restraints weight = 31645.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.115668 restraints weight = 14502.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.117634 restraints weight = 8262.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.119031 restraints weight = 5516.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.119860 restraints weight = 4106.438| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5746 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 14135 Z= 0.223 Angle : 0.862 14.981 19221 Z= 0.428 Chirality : 0.050 0.696 2252 Planarity : 0.005 0.057 2397 Dihedral : 6.473 90.120 1996 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 4.50 % Allowed : 13.29 % Favored : 82.21 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.67 (0.19), residues: 1734 helix: 0.10 (0.15), residues: 1068 sheet: None (None), residues: 0 loop : -3.21 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 265 TYR 0.030 0.002 TYR D 579 PHE 0.034 0.002 PHE A 294 TRP 0.041 0.002 TRP B 166 HIS 0.014 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00476 (14114) covalent geometry : angle 0.85858 (19185) SS BOND : bond 0.00956 ( 12) SS BOND : angle 1.85407 ( 24) hydrogen bonds : bond 0.04795 ( 758) hydrogen bonds : angle 4.45349 ( 2235) Misc. bond : bond 0.00321 ( 5) link_BETA1-4 : bond 0.06736 ( 2) link_BETA1-4 : angle 1.80253 ( 6) link_NAG-ASN : bond 0.01412 ( 2) link_NAG-ASN : angle 2.49591 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 300 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7498 (tpp) cc_final: 0.5923 (tpp) REVERT: A 168 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6950 (tm-30) REVERT: A 228 TYR cc_start: 0.5798 (t80) cc_final: 0.5549 (t80) REVERT: A 262 MET cc_start: 0.7319 (mmp) cc_final: 0.7090 (mmp) REVERT: B 192 LEU cc_start: 0.8111 (tp) cc_final: 0.7612 (mp) REVERT: B 255 CYS cc_start: 0.3156 (OUTLIER) cc_final: 0.2844 (t) REVERT: B 281 ASP cc_start: 0.7008 (p0) cc_final: 0.6531 (p0) REVERT: C 127 TRP cc_start: 0.5713 (m100) cc_final: 0.5490 (m-10) REVERT: C 366 GLU cc_start: 0.6834 (mp0) cc_final: 0.6580 (mp0) REVERT: C 462 MET cc_start: 0.4598 (tpp) cc_final: 0.4360 (tpp) REVERT: C 599 GLU cc_start: 0.5564 (OUTLIER) cc_final: 0.4674 (pm20) REVERT: C 781 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6769 (pt) REVERT: D 143 PHE cc_start: 0.7853 (t80) cc_final: 0.6052 (m-10) REVERT: D 368 MET cc_start: 0.7003 (mtt) cc_final: 0.6481 (mpp) REVERT: D 407 ILE cc_start: 0.6553 (mp) cc_final: 0.5648 (mt) REVERT: D 615 HIS cc_start: 0.6024 (t-90) cc_final: 0.5472 (t-90) REVERT: D 741 MET cc_start: 0.7763 (ppp) cc_final: 0.6736 (ppp) REVERT: D 766 LEU cc_start: 0.3654 (mt) cc_final: 0.2289 (mp) outliers start: 67 outliers final: 30 residues processed: 335 average time/residue: 0.0926 time to fit residues: 49.2390 Evaluate side-chains 274 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 630 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 33 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 167 optimal weight: 0.4980 chunk 87 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 HIS ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN D 479 HIS D 623 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.129407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.113384 restraints weight = 31716.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.116587 restraints weight = 14605.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.118677 restraints weight = 8356.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.120046 restraints weight = 5574.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.120916 restraints weight = 4146.125| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.6707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 14135 Z= 0.154 Angle : 0.760 10.478 19221 Z= 0.377 Chirality : 0.045 0.252 2252 Planarity : 0.004 0.044 2397 Dihedral : 5.711 68.329 1996 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.03 % Allowed : 14.83 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.16 (0.20), residues: 1734 helix: 0.54 (0.16), residues: 1070 sheet: -4.32 (1.62), residues: 10 loop : -3.04 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 526 TYR 0.017 0.002 TYR D 99 PHE 0.031 0.002 PHE A 294 TRP 0.027 0.002 TRP C 325 HIS 0.013 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00339 (14114) covalent geometry : angle 0.75559 (19185) SS BOND : bond 0.00396 ( 12) SS BOND : angle 1.42534 ( 24) hydrogen bonds : bond 0.04208 ( 758) hydrogen bonds : angle 4.14204 ( 2235) Misc. bond : bond 0.00515 ( 5) link_BETA1-4 : bond 0.00424 ( 2) link_BETA1-4 : angle 2.89967 ( 6) link_NAG-ASN : bond 0.00785 ( 2) link_NAG-ASN : angle 2.68850 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 285 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7454 (tpp) cc_final: 0.5921 (tpp) REVERT: A 168 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7205 (tm-30) REVERT: A 229 LYS cc_start: 0.5881 (pttp) cc_final: 0.5550 (tmtt) REVERT: A 240 LYS cc_start: 0.5743 (pttp) cc_final: 0.5503 (ptmt) REVERT: B 152 MET cc_start: 0.5905 (ptm) cc_final: 0.5467 (ptm) REVERT: B 281 ASP cc_start: 0.7048 (p0) cc_final: 0.6578 (p0) REVERT: C 95 GLU cc_start: 0.5099 (mp0) cc_final: 0.4454 (tt0) REVERT: C 127 TRP cc_start: 0.6278 (m100) cc_final: 0.6048 (m-10) REVERT: C 462 MET cc_start: 0.4885 (tpp) cc_final: 0.4646 (tpp) REVERT: C 556 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6086 (mt) REVERT: C 599 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5239 (pm20) REVERT: D 301 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6815 (t80) REVERT: D 407 ILE cc_start: 0.6684 (mp) cc_final: 0.6410 (mt) REVERT: D 571 MET cc_start: 0.5348 (OUTLIER) cc_final: 0.4925 (tpp) REVERT: D 606 ILE cc_start: 0.6480 (OUTLIER) cc_final: 0.6137 (mt) REVERT: D 741 MET cc_start: 0.7615 (ppp) cc_final: 0.6881 (tmm) REVERT: D 766 LEU cc_start: 0.4156 (OUTLIER) cc_final: 0.2814 (mp) outliers start: 60 outliers final: 27 residues processed: 320 average time/residue: 0.0966 time to fit residues: 48.0666 Evaluate side-chains 281 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 571 MET Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 766 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 9 optimal weight: 0.0040 chunk 11 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 HIS D 768 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.129678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.113161 restraints weight = 31855.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.116414 restraints weight = 14417.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.118505 restraints weight = 8222.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.119851 restraints weight = 5500.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.120784 restraints weight = 4134.542| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.7609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 14135 Z= 0.149 Angle : 0.739 8.768 19221 Z= 0.363 Chirality : 0.044 0.300 2252 Planarity : 0.004 0.044 2397 Dihedral : 5.537 58.588 1996 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.56 % Allowed : 16.58 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1734 helix: 0.68 (0.16), residues: 1084 sheet: -4.12 (1.59), residues: 10 loop : -3.05 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 362 TYR 0.019 0.001 TYR D 99 PHE 0.036 0.002 PHE A 193 TRP 0.025 0.002 TRP C 541 HIS 0.008 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00328 (14114) covalent geometry : angle 0.73748 (19185) SS BOND : bond 0.00207 ( 12) SS BOND : angle 1.03240 ( 24) hydrogen bonds : bond 0.03944 ( 758) hydrogen bonds : angle 3.98042 ( 2235) Misc. bond : bond 0.00417 ( 5) link_BETA1-4 : bond 0.01471 ( 2) link_BETA1-4 : angle 1.37894 ( 6) link_NAG-ASN : bond 0.01347 ( 2) link_NAG-ASN : angle 2.42842 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 294 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7751 (tpp) cc_final: 0.6273 (tpp) REVERT: A 168 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7419 (tm-30) REVERT: A 229 LYS cc_start: 0.5952 (pttp) cc_final: 0.5681 (tmtt) REVERT: B 123 VAL cc_start: 0.7037 (m) cc_final: 0.6829 (p) REVERT: B 152 MET cc_start: 0.6316 (ptm) cc_final: 0.5928 (ptm) REVERT: B 160 GLU cc_start: 0.5823 (tp30) cc_final: 0.5586 (tp30) REVERT: B 229 LYS cc_start: 0.7039 (tttm) cc_final: 0.6752 (pptt) REVERT: B 281 ASP cc_start: 0.7195 (p0) cc_final: 0.6581 (p0) REVERT: C 95 GLU cc_start: 0.5497 (mp0) cc_final: 0.4953 (tt0) REVERT: C 127 TRP cc_start: 0.6716 (m100) cc_final: 0.6254 (m-10) REVERT: C 556 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6560 (mt) REVERT: C 599 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5489 (pm20) REVERT: D 250 MET cc_start: 0.5421 (mtp) cc_final: 0.5220 (mtp) REVERT: D 739 GLU cc_start: 0.7566 (mp0) cc_final: 0.7232 (mp0) REVERT: D 741 MET cc_start: 0.7682 (ppp) cc_final: 0.7037 (tmm) REVERT: D 756 ARG cc_start: 0.7063 (mmp80) cc_final: 0.6028 (mtt180) outliers start: 53 outliers final: 26 residues processed: 321 average time/residue: 0.0926 time to fit residues: 46.1234 Evaluate side-chains 281 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 598 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 6 optimal weight: 8.9990 chunk 160 optimal weight: 0.0980 chunk 56 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN C 468 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 GLN ** D 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 HIS D 768 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.134647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.118864 restraints weight = 32255.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.121911 restraints weight = 15524.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.123886 restraints weight = 9139.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.125113 restraints weight = 6236.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.126016 restraints weight = 4786.434| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.8278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14135 Z= 0.141 Angle : 0.730 9.104 19221 Z= 0.358 Chirality : 0.044 0.261 2252 Planarity : 0.004 0.048 2397 Dihedral : 5.396 52.305 1996 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.29 % Allowed : 18.32 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1734 helix: 0.86 (0.16), residues: 1076 sheet: -3.27 (3.18), residues: 5 loop : -2.90 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 362 TYR 0.023 0.002 TYR D 99 PHE 0.032 0.002 PHE A 193 TRP 0.022 0.002 TRP A 269 HIS 0.005 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00311 (14114) covalent geometry : angle 0.72728 (19185) SS BOND : bond 0.00308 ( 12) SS BOND : angle 1.15233 ( 24) hydrogen bonds : bond 0.03850 ( 758) hydrogen bonds : angle 3.94228 ( 2235) Misc. bond : bond 0.00494 ( 5) link_BETA1-4 : bond 0.01278 ( 2) link_BETA1-4 : angle 1.95740 ( 6) link_NAG-ASN : bond 0.00902 ( 2) link_NAG-ASN : angle 2.26007 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 286 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.7923 (mmtt) cc_final: 0.6851 (mmmt) REVERT: A 152 MET cc_start: 0.7962 (tpp) cc_final: 0.6598 (tpp) REVERT: A 262 MET cc_start: 0.7491 (mmm) cc_final: 0.7180 (mmp) REVERT: B 123 VAL cc_start: 0.7019 (m) cc_final: 0.6816 (p) REVERT: B 281 ASP cc_start: 0.7038 (p0) cc_final: 0.6577 (p0) REVERT: C 127 TRP cc_start: 0.7093 (m100) cc_final: 0.6460 (m-10) REVERT: C 550 MET cc_start: 0.7413 (mmp) cc_final: 0.7201 (mmp) REVERT: C 556 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.7031 (tp) REVERT: C 599 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5469 (pm20) REVERT: D 739 GLU cc_start: 0.7535 (mp0) cc_final: 0.7231 (mp0) REVERT: D 741 MET cc_start: 0.7580 (ppp) cc_final: 0.6854 (ppp) REVERT: D 756 ARG cc_start: 0.7235 (mmp80) cc_final: 0.6278 (mtt180) REVERT: D 768 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.7207 (m90) outliers start: 49 outliers final: 29 residues processed: 315 average time/residue: 0.0846 time to fit residues: 42.8662 Evaluate side-chains 295 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 37 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 121 optimal weight: 0.2980 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 21 optimal weight: 0.0570 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 203 ASN B 223 ASN C 214 ASN C 659 ASN D 442 GLN D 623 HIS D 768 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.135806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.120498 restraints weight = 31698.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.123507 restraints weight = 15208.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.125461 restraints weight = 8919.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.126751 restraints weight = 6045.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.127591 restraints weight = 4560.589| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.8691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14135 Z= 0.132 Angle : 0.733 12.585 19221 Z= 0.353 Chirality : 0.044 0.228 2252 Planarity : 0.004 0.048 2397 Dihedral : 5.466 48.401 1996 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.09 % Allowed : 19.73 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.50 (0.21), residues: 1734 helix: 1.09 (0.16), residues: 1068 sheet: None (None), residues: 0 loop : -2.84 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 767 TYR 0.025 0.001 TYR C 397 PHE 0.028 0.002 PHE A 193 TRP 0.032 0.002 TRP A 269 HIS 0.037 0.001 HIS D 768 Details of bonding type rmsd covalent geometry : bond 0.00286 (14114) covalent geometry : angle 0.73133 (19185) SS BOND : bond 0.00285 ( 12) SS BOND : angle 1.02809 ( 24) hydrogen bonds : bond 0.03696 ( 758) hydrogen bonds : angle 3.85533 ( 2235) Misc. bond : bond 0.00244 ( 5) link_BETA1-4 : bond 0.00845 ( 2) link_BETA1-4 : angle 1.69492 ( 6) link_NAG-ASN : bond 0.00239 ( 2) link_NAG-ASN : angle 2.32226 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 281 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7894 (tpp) cc_final: 0.6202 (tpp) REVERT: A 262 MET cc_start: 0.7656 (mmm) cc_final: 0.7365 (mmp) REVERT: B 123 VAL cc_start: 0.7143 (m) cc_final: 0.6920 (p) REVERT: B 281 ASP cc_start: 0.6944 (p0) cc_final: 0.6541 (p0) REVERT: C 127 TRP cc_start: 0.7238 (m100) cc_final: 0.6411 (m-10) REVERT: C 332 MET cc_start: 0.7468 (tpt) cc_final: 0.6946 (mmt) REVERT: C 556 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7250 (tp) REVERT: C 599 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5493 (pm20) REVERT: D 462 MET cc_start: 0.8549 (mmt) cc_final: 0.8322 (mmt) REVERT: D 739 GLU cc_start: 0.7558 (mp0) cc_final: 0.7240 (mp0) REVERT: D 756 ARG cc_start: 0.7171 (mmp80) cc_final: 0.6343 (mtt180) outliers start: 46 outliers final: 33 residues processed: 307 average time/residue: 0.0982 time to fit residues: 46.8007 Evaluate side-chains 296 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 659 ASN Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 45 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.0170 chunk 47 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 145 optimal weight: 0.0170 chunk 148 optimal weight: 5.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN D 623 HIS D 768 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.135156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.119045 restraints weight = 32319.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.122186 restraints weight = 15164.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.124184 restraints weight = 8829.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.125512 restraints weight = 5978.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.126333 restraints weight = 4526.995| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.9008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14135 Z= 0.131 Angle : 0.744 13.608 19221 Z= 0.355 Chirality : 0.044 0.292 2252 Planarity : 0.004 0.047 2397 Dihedral : 5.282 42.935 1996 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.28 % Allowed : 21.74 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.38 (0.21), residues: 1734 helix: 1.15 (0.16), residues: 1067 sheet: None (None), residues: 0 loop : -2.72 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 225 TYR 0.026 0.001 TYR C 397 PHE 0.055 0.002 PHE A 193 TRP 0.019 0.001 TRP C 541 HIS 0.003 0.000 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00288 (14114) covalent geometry : angle 0.74056 (19185) SS BOND : bond 0.00240 ( 12) SS BOND : angle 0.96933 ( 24) hydrogen bonds : bond 0.03625 ( 758) hydrogen bonds : angle 3.84188 ( 2235) Misc. bond : bond 0.00137 ( 5) link_BETA1-4 : bond 0.01024 ( 2) link_BETA1-4 : angle 3.39189 ( 6) link_NAG-ASN : bond 0.00482 ( 2) link_NAG-ASN : angle 2.54854 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 284 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7156 (ptm-80) cc_final: 0.6813 (ptm-80) REVERT: A 152 MET cc_start: 0.8013 (tpp) cc_final: 0.6255 (tpp) REVERT: A 167 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7844 (mp10) REVERT: A 305 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.6647 (tp) REVERT: B 123 VAL cc_start: 0.7128 (m) cc_final: 0.6908 (p) REVERT: B 281 ASP cc_start: 0.7105 (p0) cc_final: 0.6768 (p0) REVERT: C 127 TRP cc_start: 0.7359 (m100) cc_final: 0.6347 (m-10) REVERT: C 157 ARG cc_start: 0.7408 (ttp80) cc_final: 0.7168 (ttp-110) REVERT: C 332 MET cc_start: 0.7597 (tpt) cc_final: 0.6915 (mmt) REVERT: C 556 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7079 (mt) REVERT: C 599 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.5677 (pm20) REVERT: D 109 GLU cc_start: 0.6342 (mm-30) cc_final: 0.6065 (mp0) REVERT: D 497 TYR cc_start: 0.7473 (t80) cc_final: 0.7141 (t80) REVERT: D 595 ASP cc_start: 0.7828 (p0) cc_final: 0.7614 (m-30) REVERT: D 739 GLU cc_start: 0.7657 (mp0) cc_final: 0.7275 (mp0) REVERT: D 741 MET cc_start: 0.7689 (ppp) cc_final: 0.7210 (ppp) REVERT: D 756 ARG cc_start: 0.7279 (mmp80) cc_final: 0.6489 (mtt180) outliers start: 34 outliers final: 26 residues processed: 302 average time/residue: 0.0979 time to fit residues: 46.2422 Evaluate side-chains 295 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 266 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 62 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 169 optimal weight: 0.0070 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 170 optimal weight: 0.0770 chunk 49 optimal weight: 0.4980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN ** C 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN C 659 ASN ** D 162 ASN ** 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 = 0.3992 r_free = 0.3992 target = 0.135407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.119176 restraints weight = 32727.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.122329 restraints weight = 15337.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.124354 restraints weight = 8922.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.125679 restraints weight = 6029.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.126540 restraints weight = 4566.036| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.9470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14135 Z= 0.133 Angle : 0.765 17.525 19221 Z= 0.362 Chirality : 0.044 0.253 2252 Planarity : 0.004 0.050 2397 Dihedral : 5.159 35.721 1996 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.28 % Allowed : 22.35 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.24 (0.21), residues: 1734 helix: 1.21 (0.16), residues: 1072 sheet: None (None), residues: 0 loop : -2.59 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 362 TYR 0.023 0.001 TYR C 397 PHE 0.043 0.002 PHE A 119 TRP 0.018 0.001 TRP C 541 HIS 0.006 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00293 (14114) covalent geometry : angle 0.76298 (19185) SS BOND : bond 0.00228 ( 12) SS BOND : angle 0.81545 ( 24) hydrogen bonds : bond 0.03695 ( 758) hydrogen bonds : angle 3.80721 ( 2235) Misc. bond : bond 0.00169 ( 5) link_BETA1-4 : bond 0.01121 ( 2) link_BETA1-4 : angle 2.65585 ( 6) link_NAG-ASN : bond 0.00199 ( 2) link_NAG-ASN : angle 1.78753 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 294 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7974 (tpp) cc_final: 0.6133 (tpp) REVERT: A 167 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7869 (mm-40) REVERT: B 281 ASP cc_start: 0.7125 (p0) cc_final: 0.6815 (p0) REVERT: C 127 TRP cc_start: 0.7512 (m100) cc_final: 0.6377 (m-10) REVERT: C 505 TYR cc_start: 0.7563 (t80) cc_final: 0.6923 (t80) REVERT: C 599 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5873 (pm20) REVERT: D 497 TYR cc_start: 0.7699 (t80) cc_final: 0.7380 (t80) REVERT: D 739 GLU cc_start: 0.7650 (mp0) cc_final: 0.7262 (mp0) REVERT: D 741 MET cc_start: 0.7515 (ppp) cc_final: 0.6998 (ppp) REVERT: D 756 ARG cc_start: 0.7276 (mmp80) cc_final: 0.6604 (mtt180) outliers start: 34 outliers final: 26 residues processed: 311 average time/residue: 0.0944 time to fit residues: 45.8809 Evaluate side-chains 295 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 659 ASN Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 154 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 138 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.134556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.118766 restraints weight = 31900.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.121800 restraints weight = 14793.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.123764 restraints weight = 8521.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.124974 restraints weight = 5727.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.125879 restraints weight = 4372.014| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.9927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 14135 Z= 0.139 Angle : 0.770 13.851 19221 Z= 0.369 Chirality : 0.044 0.224 2252 Planarity : 0.004 0.046 2397 Dihedral : 5.043 35.741 1996 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.74 % Allowed : 23.62 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.21), residues: 1734 helix: 1.26 (0.16), residues: 1072 sheet: None (None), residues: 0 loop : -2.58 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 110 TYR 0.023 0.001 TYR C 397 PHE 0.031 0.002 PHE A 119 TRP 0.035 0.001 TRP A 269 HIS 0.011 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00314 (14114) covalent geometry : angle 0.76753 (19185) SS BOND : bond 0.00296 ( 12) SS BOND : angle 1.04518 ( 24) hydrogen bonds : bond 0.03724 ( 758) hydrogen bonds : angle 3.82715 ( 2235) Misc. bond : bond 0.00111 ( 5) link_BETA1-4 : bond 0.00242 ( 2) link_BETA1-4 : angle 2.43345 ( 6) link_NAG-ASN : bond 0.00347 ( 2) link_NAG-ASN : angle 1.97711 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 290 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7979 (tpp) cc_final: 0.6607 (tpp) REVERT: A 167 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7872 (mm-40) REVERT: B 241 MET cc_start: 0.6642 (ppp) cc_final: 0.6390 (ppp) REVERT: B 281 ASP cc_start: 0.7109 (p0) cc_final: 0.6831 (p0) REVERT: C 127 TRP cc_start: 0.7679 (m100) cc_final: 0.6430 (m-10) REVERT: C 398 TRP cc_start: 0.5717 (OUTLIER) cc_final: 0.5507 (m-90) REVERT: C 505 TYR cc_start: 0.7558 (t80) cc_final: 0.6703 (t80) REVERT: C 599 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.5999 (pm20) REVERT: D 109 GLU cc_start: 0.6420 (mm-30) cc_final: 0.6160 (mp0) REVERT: D 462 MET cc_start: 0.8551 (mmm) cc_final: 0.8252 (mmt) REVERT: D 497 TYR cc_start: 0.7872 (t80) cc_final: 0.7593 (t80) REVERT: D 739 GLU cc_start: 0.7569 (mp0) cc_final: 0.7231 (mp0) REVERT: D 756 ARG cc_start: 0.7304 (mmp80) cc_final: 0.6842 (mtt180) outliers start: 26 outliers final: 20 residues processed: 304 average time/residue: 0.0916 time to fit residues: 43.9060 Evaluate side-chains 295 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 273 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 398 TRP Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 66 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.0670 chunk 25 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 468 ASN ** C 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.134474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.118053 restraints weight = 32663.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.121154 restraints weight = 15360.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.123143 restraints weight = 8990.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.124390 restraints weight = 6105.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.125238 restraints weight = 4692.673| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 1.0576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 14135 Z= 0.142 Angle : 0.783 12.522 19221 Z= 0.376 Chirality : 0.045 0.204 2252 Planarity : 0.004 0.048 2397 Dihedral : 4.975 39.673 1996 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.68 % Allowed : 24.50 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1734 helix: 1.26 (0.16), residues: 1073 sheet: None (None), residues: 0 loop : -2.52 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 107 TYR 0.030 0.002 TYR C 397 PHE 0.032 0.001 PHE D 528 TRP 0.016 0.001 TRP C 541 HIS 0.006 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00320 (14114) covalent geometry : angle 0.78143 (19185) SS BOND : bond 0.00235 ( 12) SS BOND : angle 0.97652 ( 24) hydrogen bonds : bond 0.03822 ( 758) hydrogen bonds : angle 3.93679 ( 2235) Misc. bond : bond 0.00121 ( 5) link_BETA1-4 : bond 0.00646 ( 2) link_BETA1-4 : angle 1.92632 ( 6) link_NAG-ASN : bond 0.00271 ( 2) link_NAG-ASN : angle 1.89524 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2320.04 seconds wall clock time: 40 minutes 43.36 seconds (2443.36 seconds total)