Starting phenix.real_space_refine on Fri Jul 3 11:40:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cq7_30438/07_2026/7cq7_30438.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cq7_30438/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7cq7_30438/07_2026/7cq7_30438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cq7_30438/07_2026/7cq7_30438.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cq7_30438/07_2026/7cq7_30438.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cq7_30438/07_2026/7cq7_30438.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cq7_30438/07_2026/7cq7_30438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cq7_30438/07_2026/7cq7_30438.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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: 2.52, per 1000 atoms: 0.18 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: 1.02 Conformation dependent library (CDL) restraints added in 444.4 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: 0.23 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: 1.68 Time building geometry restraints manager: 1.31 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: 8137 22.84 - 45.68: 174 45.68 - 68.52: 10 68.52 - 91.36: 8 91.36 - 114.20: 1 Dihedral angle restraints: 8330 sinusoidal: 3215 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 8327 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: 1.560 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.260 Find NCS groups from input model: 0.350 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: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4205 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 : 10.328 114.200 4982 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/Z covalent geometry : bond 0.00804 / 0.35 (14114) covalent geometry : angle 1.06949 / 0.57 (19185) SS BOND : bond 0.00331 / 0.20 ( 12) SS BOND : angle 1.82474 / 1.06 ( 24) hydrogen bonds : bond 0.20482 / 13.70 ( 758) hydrogen bonds : angle 7.64867 / 5.39 ( 2235) Misc. bond : bond 0.32045 / 17.30 ( 5) link_BETA1-4 : bond 0.00595 / 0.30 ( 2) link_BETA1-4 : angle 2.74501 / 1.50 ( 6) link_NAG-ASN : bond 0.00305 / 0.16 ( 2) link_NAG-ASN : angle 3.75561 / 2.03 ( 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 : 0.328 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: 0.0988 time to fit residues: 66.9633 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 : 0.317 ------------------------------------------------------------------------------- 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... ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN A 202 HIS 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 = 0.3880 r_free = 0.3880 target = 0.129371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.113414 restraints weight = 31640.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.116620 restraints weight = 14417.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.118663 restraints weight = 8190.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.119928 restraints weight = 5433.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.120893 restraints weight = 4091.153| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4983 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14135 Z= 0.172 Angle : 0.838 12.423 19221 Z= 0.414 Chirality : 0.046 0.445 2252 Planarity : 0.006 0.052 2397 Dihedral : 6.661 108.151 1912 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.15 % Allowed : 11.61 % Favored : 85.23 % 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: -2.42 (0.18), residues: 1734 helix: -0.47 (0.15), residues: 1070 sheet: None (None), residues: 0 loop : -3.57 (0.20), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 362 TYR 0.016 0.002 TYR C 547 PHE 0.034 0.002 PHE A 294 TRP 0.031 0.002 TRP D 179 HIS 0.009 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (14114) covalent geometry : angle 0.83103 / 0.41 (19185) SS BOND : bond 0.00667 / 0.40 ( 12) SS BOND : angle 2.30014 / 1.58 ( 24) hydrogen bonds : bond 0.05110 / 3.37 ( 758) hydrogen bonds : angle 4.70912 / 3.33 ( 2235) Misc. bond : bond 0.00589 / 0.31 ( 5) link_BETA1-4 : bond 0.00297 / 0.16 ( 2) link_BETA1-4 : angle 1.62489 / 0.91 ( 6) link_NAG-ASN : bond 0.00668 / 0.35 ( 2) link_NAG-ASN : angle 3.93692 / 1.99 ( 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 335 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 288 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7259 (tpp) cc_final: 0.5548 (tpp) REVERT: A 168 GLU cc_start: 0.6519 (tm-30) cc_final: 0.6143 (tm-30) REVERT: A 304 PHE cc_start: 0.7149 (t80) cc_final: 0.6933 (t80) REVERT: B 188 TYR cc_start: 0.6144 (t80) cc_final: 0.5915 (m-10) REVERT: B 192 LEU cc_start: 0.8447 (tp) cc_final: 0.7761 (mp) REVERT: B 255 CYS cc_start: 0.3226 (OUTLIER) cc_final: 0.2636 (t) REVERT: B 281 ASP cc_start: 0.6923 (p0) cc_final: 0.6667 (p0) REVERT: C 323 LEU cc_start: 0.4485 (OUTLIER) cc_final: 0.3496 (mt) REVERT: C 399 LEU cc_start: 0.6610 (tp) cc_final: 0.6087 (tt) REVERT: C 433 TYR cc_start: 0.6501 (OUTLIER) cc_final: 0.6210 (t80) REVERT: C 570 MET cc_start: 0.5633 (mmp) cc_final: 0.5370 (mmp) REVERT: C 588 MET cc_start: 0.5571 (mtp) cc_final: 0.4790 (ppp) REVERT: C 599 GLU cc_start: 0.4597 (OUTLIER) cc_final: 0.3362 (pm20) REVERT: C 659 ASN cc_start: 0.3934 (m-40) cc_final: 0.2985 (m110) REVERT: D 99 TYR cc_start: 0.6409 (t80) cc_final: 0.6056 (t80) REVERT: D 132 LEU cc_start: 0.7606 (mt) cc_final: 0.7395 (mt) REVERT: D 143 PHE cc_start: 0.7611 (t80) cc_final: 0.5915 (m-10) REVERT: D 275 ILE cc_start: 0.6042 (tp) cc_final: 0.5463 (mp) REVERT: D 368 MET cc_start: 0.6268 (mtt) cc_final: 0.5335 (mpp) REVERT: D 598 ILE cc_start: 0.7972 (mm) cc_final: 0.7735 (mm) outliers start: 47 outliers final: 20 residues processed: 317 average time/residue: 0.0813 time to fit residues: 40.6799 Evaluate side-chains 253 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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: 4.9990 chunk 92 optimal weight: 0.0770 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 GLN B 113 GLN B 173 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 HIS D 623 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.131191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.115800 restraints weight = 31404.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.118973 restraints weight = 14485.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.120946 restraints weight = 8260.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.122347 restraints weight = 5471.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.123058 restraints weight = 4041.841| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5357 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14135 Z= 0.167 Angle : 0.780 11.442 19221 Z= 0.384 Chirality : 0.045 0.328 2252 Planarity : 0.005 0.044 2397 Dihedral : 5.972 90.363 1912 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.83 % Allowed : 13.56 % Favored : 82.62 % 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: -1.57 (0.19), residues: 1734 helix: 0.20 (0.16), residues: 1070 sheet: None (None), residues: 0 loop : -3.23 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 362 TYR 0.024 0.002 TYR D 397 PHE 0.035 0.002 PHE A 294 TRP 0.027 0.002 TRP B 166 HIS 0.012 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (14114) covalent geometry : angle 0.77617 / 0.38 (19185) SS BOND : bond 0.00444 / 0.27 ( 12) SS BOND : angle 1.88162 / 1.55 ( 24) hydrogen bonds : bond 0.04510 / 3.00 ( 758) hydrogen bonds : angle 4.31947 / 3.06 ( 2235) Misc. bond : bond 0.00282 / 0.17 ( 5) link_BETA1-4 : bond 0.01159 / 0.61 ( 2) link_BETA1-4 : angle 1.69565 / 0.85 ( 6) link_NAG-ASN : bond 0.01497 / 0.79 ( 2) link_NAG-ASN : angle 2.23764 / 1.11 ( 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 337 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7245 (tpp) cc_final: 0.5922 (tpp) REVERT: A 168 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6598 (tm-30) REVERT: B 152 MET cc_start: 0.5244 (ptm) cc_final: 0.4858 (ptm) REVERT: B 188 TYR cc_start: 0.6206 (t80) cc_final: 0.5921 (m-10) REVERT: B 192 LEU cc_start: 0.8309 (tp) cc_final: 0.7577 (mp) REVERT: B 255 CYS cc_start: 0.3341 (OUTLIER) cc_final: 0.2893 (t) REVERT: B 281 ASP cc_start: 0.6915 (p0) cc_final: 0.6510 (p0) REVERT: C 323 LEU cc_start: 0.5398 (OUTLIER) cc_final: 0.4802 (mt) REVERT: C 462 MET cc_start: 0.3937 (tpp) cc_final: 0.3713 (tpp) REVERT: C 588 MET cc_start: 0.5680 (mtp) cc_final: 0.4884 (ppp) REVERT: C 599 GLU cc_start: 0.5089 (OUTLIER) cc_final: 0.4031 (pm20) REVERT: C 781 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6476 (pt) REVERT: D 132 LEU cc_start: 0.7857 (mt) cc_final: 0.7601 (mt) REVERT: D 143 PHE cc_start: 0.7679 (t80) cc_final: 0.5825 (m-10) REVERT: D 368 MET cc_start: 0.6810 (mtt) cc_final: 0.6598 (mtm) REVERT: D 615 HIS cc_start: 0.5952 (t-90) cc_final: 0.5343 (t-90) REVERT: D 741 MET cc_start: 0.7596 (ppp) cc_final: 0.6806 (tmm) REVERT: D 766 LEU cc_start: 0.3544 (OUTLIER) cc_final: 0.2148 (mp) outliers start: 57 outliers final: 25 residues processed: 311 average time/residue: 0.0793 time to fit residues: 39.2338 Evaluate side-chains 265 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU 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 229 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 500 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 678 LEU 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 244 VAL 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 766 LEU Chi-restraints excluded: chain D residue 787 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 152 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN C 468 ASN ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 605 HIS C 683 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN D 451 GLN D 479 HIS ** D 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 HIS ** D 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.130187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.115156 restraints weight = 32642.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.118109 restraints weight = 15357.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.119988 restraints weight = 8844.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.121251 restraints weight = 5913.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.122046 restraints weight = 4415.835| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 1.0123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.181 14135 Z= 0.318 Angle : 1.097 16.962 19221 Z= 0.565 Chirality : 0.058 0.453 2252 Planarity : 0.007 0.056 2397 Dihedral : 6.472 56.363 1912 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 5.17 % Allowed : 13.56 % Favored : 81.28 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.12 % 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: -2.30 (0.19), residues: 1734 helix: -0.53 (0.15), residues: 1071 sheet: -3.29 (1.16), residues: 14 loop : -3.20 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 265 TYR 0.036 0.003 TYR C 156 PHE 0.058 0.004 PHE B 161 TRP 0.048 0.004 TRP C 325 HIS 0.011 0.002 HIS D 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.32 (14114) covalent geometry : angle 1.08807 / 0.56 (19185) SS BOND : bond 0.00719 / 0.48 ( 12) SS BOND : angle 2.57805 / 2.12 ( 24) hydrogen bonds : bond 0.06046 / 4.11 ( 758) hydrogen bonds : angle 5.11602 / 3.63 ( 2235) Misc. bond : bond 0.00564 / 0.28 ( 5) link_BETA1-4 : bond 0.00398 / 0.19 ( 2) link_BETA1-4 : angle 5.51656 / 2.35 ( 6) link_NAG-ASN : bond 0.01124 / 0.59 ( 2) link_NAG-ASN : angle 3.06889 / 1.61 ( 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 494 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 417 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8015 (tpp) cc_final: 0.7294 (tpp) REVERT: A 168 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7318 (tm-30) REVERT: A 240 LYS cc_start: 0.6090 (pttp) cc_final: 0.5798 (ptmm) REVERT: B 152 MET cc_start: 0.6977 (ptm) cc_final: 0.6664 (ptm) REVERT: B 281 ASP cc_start: 0.7243 (p0) cc_final: 0.6508 (p0) REVERT: C 126 ARG cc_start: 0.8254 (mtt90) cc_final: 0.7765 (mpt-90) REVERT: C 127 TRP cc_start: 0.8149 (m100) cc_final: 0.7138 (m-10) REVERT: C 160 LYS cc_start: 0.7720 (tttt) cc_final: 0.7411 (tmtt) REVERT: C 281 ARG cc_start: 0.5618 (mtm110) cc_final: 0.5361 (mtm110) REVERT: C 305 VAL cc_start: 0.9129 (t) cc_final: 0.8817 (p) REVERT: C 398 TRP cc_start: 0.6089 (OUTLIER) cc_final: 0.5779 (m-90) REVERT: C 599 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: C 760 LEU cc_start: 0.8608 (tp) cc_final: 0.8402 (tp) REVERT: D 220 HIS cc_start: 0.7001 (m-70) cc_final: 0.6740 (m-70) REVERT: D 407 ILE cc_start: 0.7568 (mp) cc_final: 0.7230 (mt) REVERT: D 459 TYR cc_start: 0.7213 (m-80) cc_final: 0.7012 (m-80) REVERT: D 460 ASN cc_start: 0.7695 (t0) cc_final: 0.7315 (t0) REVERT: D 486 ASN cc_start: 0.8069 (t0) cc_final: 0.7807 (t0) REVERT: D 606 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7424 (mt) REVERT: D 741 MET cc_start: 0.7623 (ppp) cc_final: 0.7094 (ppp) REVERT: D 756 ARG cc_start: 0.7156 (mmp80) cc_final: 0.6822 (mtt180) outliers start: 77 outliers final: 31 residues processed: 463 average time/residue: 0.0872 time to fit residues: 61.8917 Evaluate side-chains 337 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 303 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 398 TRP Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 297 VAL 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 519 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 787 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 116 optimal weight: 0.0980 chunk 93 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 HIS ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN C 683 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 HIS ** D 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.124741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.108617 restraints weight = 32810.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.111490 restraints weight = 15543.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.113332 restraints weight = 9117.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.114505 restraints weight = 6217.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.115356 restraints weight = 4786.154| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 1.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 14135 Z= 0.234 Angle : 0.863 14.072 19221 Z= 0.431 Chirality : 0.050 0.370 2252 Planarity : 0.005 0.080 2397 Dihedral : 5.798 72.775 1912 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.43 % Allowed : 20.07 % Favored : 75.50 % 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: -1.44 (0.20), residues: 1734 helix: 0.29 (0.15), residues: 1073 sheet: None (None), residues: 0 loop : -3.15 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 362 TYR 0.026 0.002 TYR B 188 PHE 0.025 0.002 PHE A 291 TRP 0.034 0.003 TRP B 166 HIS 0.014 0.002 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (14114) covalent geometry : angle 0.85573 / 0.43 (19185) SS BOND : bond 0.01058 / 0.65 ( 12) SS BOND : angle 1.59201 / 1.15 ( 24) hydrogen bonds : bond 0.04827 / 3.25 ( 758) hydrogen bonds : angle 4.57371 / 3.21 ( 2235) Misc. bond : bond 0.00587 / 0.29 ( 5) link_BETA1-4 : bond 0.00420 / 0.22 ( 2) link_BETA1-4 : angle 4.93762 / 2.02 ( 6) link_NAG-ASN : bond 0.01826 / 0.95 ( 2) link_NAG-ASN : angle 3.18839 / 1.50 ( 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 431 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 365 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.6984 (p0) REVERT: A 152 MET cc_start: 0.8111 (tpp) cc_final: 0.7276 (tpp) REVERT: B 107 ARG cc_start: 0.6923 (mmm160) cc_final: 0.6693 (mmm160) REVERT: B 257 ASP cc_start: 0.6964 (m-30) cc_final: 0.6616 (m-30) REVERT: B 281 ASP cc_start: 0.7370 (p0) cc_final: 0.6861 (p0) REVERT: C 160 LYS cc_start: 0.7924 (tttt) cc_final: 0.7565 (tmtt) REVERT: C 332 MET cc_start: 0.8452 (tpt) cc_final: 0.8209 (mmm) REVERT: C 401 MET cc_start: 0.7395 (mtp) cc_final: 0.7112 (mtm) REVERT: C 413 GLN cc_start: 0.8446 (mt0) cc_final: 0.7591 (mp10) REVERT: C 462 MET cc_start: 0.7126 (tpp) cc_final: 0.6847 (mmm) REVERT: C 505 TYR cc_start: 0.8181 (t80) cc_final: 0.7966 (t80) REVERT: C 599 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7390 (pm20) REVERT: C 756 ARG cc_start: 0.7635 (tpt90) cc_final: 0.7184 (tpt90) REVERT: C 767 ARG cc_start: 0.5239 (ptm160) cc_final: 0.3996 (ptm160) REVERT: D 329 PHE cc_start: 0.8214 (t80) cc_final: 0.7979 (t80) REVERT: D 459 TYR cc_start: 0.7395 (m-80) cc_final: 0.6806 (m-80) REVERT: D 571 MET cc_start: 0.7670 (tpp) cc_final: 0.7249 (mtt) REVERT: D 739 GLU cc_start: 0.7939 (mp0) cc_final: 0.7647 (mp0) outliers start: 66 outliers final: 40 residues processed: 404 average time/residue: 0.0859 time to fit residues: 53.8112 Evaluate side-chains 339 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 479 HIS Chi-restraints excluded: chain C residue 519 LEU 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 680 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 733 CYS Chi-restraints excluded: chain D residue 776 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 6 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 0.0470 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.125141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.108959 restraints weight = 32234.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111830 restraints weight = 15194.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.113669 restraints weight = 8895.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.114905 restraints weight = 6075.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.115705 restraints weight = 4654.804| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 1.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14135 Z= 0.151 Angle : 0.768 11.383 19221 Z= 0.380 Chirality : 0.046 0.306 2252 Planarity : 0.004 0.039 2397 Dihedral : 5.428 60.469 1912 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.83 % Allowed : 22.82 % Favored : 73.36 % 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: -0.98 (0.20), residues: 1734 helix: 0.66 (0.16), residues: 1071 sheet: -3.22 (3.29), residues: 5 loop : -2.96 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 756 TYR 0.028 0.002 TYR C 397 PHE 0.053 0.002 PHE A 200 TRP 0.032 0.002 TRP A 269 HIS 0.008 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (14114) covalent geometry : angle 0.76487 / 0.38 (19185) SS BOND : bond 0.01260 / 0.75 ( 12) SS BOND : angle 1.29899 / 0.74 ( 24) hydrogen bonds : bond 0.04299 / 2.86 ( 758) hydrogen bonds : angle 4.30122 / 3.03 ( 2235) Misc. bond : bond 0.00300 / 0.16 ( 5) link_BETA1-4 : bond 0.01071 / 0.55 ( 2) link_BETA1-4 : angle 2.30490 / 1.03 ( 6) link_NAG-ASN : bond 0.00918 / 0.48 ( 2) link_NAG-ASN : angle 2.51184 / 1.28 ( 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 385 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 328 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8091 (tpp) cc_final: 0.7670 (tpp) REVERT: A 153 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7044 (pt0) REVERT: A 167 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8267 (mm-40) REVERT: A 305 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7301 (tp) REVERT: B 107 ARG cc_start: 0.7033 (mmm160) cc_final: 0.6790 (mmm160) REVERT: B 254 LEU cc_start: 0.6722 (mt) cc_final: 0.6489 (mt) REVERT: B 281 ASP cc_start: 0.7320 (p0) cc_final: 0.6910 (p0) REVERT: C 157 ARG cc_start: 0.8244 (ttp80) cc_final: 0.8024 (mtm110) REVERT: C 160 LYS cc_start: 0.8074 (tttt) cc_final: 0.7743 (tmtt) REVERT: C 413 GLN cc_start: 0.8531 (mt0) cc_final: 0.7671 (mp10) REVERT: C 462 MET cc_start: 0.7125 (tpp) cc_final: 0.6915 (mmm) REVERT: C 505 TYR cc_start: 0.8200 (t80) cc_final: 0.7826 (t80) REVERT: C 599 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: C 687 LEU cc_start: 0.8452 (mp) cc_final: 0.8186 (mp) REVERT: C 741 MET cc_start: 0.7518 (mtp) cc_final: 0.7259 (mtp) REVERT: C 756 ARG cc_start: 0.7946 (tpt90) cc_final: 0.7232 (tpt90) REVERT: D 329 PHE cc_start: 0.8269 (t80) cc_final: 0.8053 (t80) REVERT: D 400 THR cc_start: 0.9006 (p) cc_final: 0.8669 (t) REVERT: D 416 GLU cc_start: 0.8811 (tp30) cc_final: 0.8531 (tp30) REVERT: D 459 TYR cc_start: 0.7373 (m-80) cc_final: 0.6771 (m-80) REVERT: D 571 MET cc_start: 0.7374 (tpp) cc_final: 0.6849 (ttm) REVERT: D 739 GLU cc_start: 0.7969 (mp0) cc_final: 0.7667 (mp0) outliers start: 57 outliers final: 33 residues processed: 363 average time/residue: 0.0838 time to fit residues: 47.2848 Evaluate side-chains 326 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 291 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 479 HIS Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 584 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 663 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 787 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 37 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 57 optimal weight: 0.0060 chunk 5 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 167 GLN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN D 442 GLN ** D 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.125523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.109301 restraints weight = 32517.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.112137 restraints weight = 15245.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.113968 restraints weight = 8961.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.115124 restraints weight = 6144.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.116006 restraints weight = 4766.706| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 1.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14135 Z= 0.144 Angle : 0.774 10.784 19221 Z= 0.376 Chirality : 0.046 0.333 2252 Planarity : 0.004 0.037 2397 Dihedral : 5.229 55.807 1912 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.82 % Allowed : 24.56 % Favored : 72.62 % 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: -0.76 (0.20), residues: 1734 helix: 0.85 (0.16), residues: 1072 sheet: None (None), residues: 0 loop : -2.92 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 756 TYR 0.023 0.001 TYR C 397 PHE 0.026 0.002 PHE A 193 TRP 0.026 0.002 TRP A 269 HIS 0.007 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (14114) covalent geometry : angle 0.77141 / 0.38 (19185) SS BOND : bond 0.00275 / 0.17 ( 12) SS BOND : angle 1.40490 / 1.53 ( 24) hydrogen bonds : bond 0.04075 / 2.69 ( 758) hydrogen bonds : angle 4.19021 / 2.95 ( 2235) Misc. bond : bond 0.00178 / 0.10 ( 5) link_BETA1-4 : bond 0.01011 / 0.52 ( 2) link_BETA1-4 : angle 2.12007 / 1.04 ( 6) link_NAG-ASN : bond 0.00663 / 0.35 ( 2) link_NAG-ASN : angle 2.37833 / 1.18 ( 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 367 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 325 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.7813 (t80) cc_final: 0.7532 (t80) REVERT: A 125 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8310 (mmtt) REVERT: A 152 MET cc_start: 0.8324 (tpp) cc_final: 0.7729 (ttp) REVERT: A 153 GLN cc_start: 0.7628 (tp-100) cc_final: 0.7244 (pt0) REVERT: B 107 ARG cc_start: 0.7050 (mmm160) cc_final: 0.6762 (mmm160) REVERT: B 262 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6395 (tpp) REVERT: B 281 ASP cc_start: 0.7272 (p0) cc_final: 0.6852 (p0) REVERT: C 160 LYS cc_start: 0.8184 (tttt) cc_final: 0.7849 (tmtt) REVERT: C 462 MET cc_start: 0.7224 (tpp) cc_final: 0.7016 (mmm) REVERT: C 505 TYR cc_start: 0.8095 (t80) cc_final: 0.7792 (t80) REVERT: C 687 LEU cc_start: 0.8450 (mp) cc_final: 0.8240 (mp) REVERT: C 741 MET cc_start: 0.7549 (mtp) cc_final: 0.7303 (mtp) REVERT: C 756 ARG cc_start: 0.8023 (tpt90) cc_final: 0.7242 (tpt90) REVERT: D 400 THR cc_start: 0.9094 (p) cc_final: 0.8734 (t) REVERT: D 550 MET cc_start: 0.9146 (mmt) cc_final: 0.8863 (mmt) REVERT: D 571 MET cc_start: 0.7453 (tpp) cc_final: 0.6984 (ttm) REVERT: D 739 GLU cc_start: 0.8013 (mp0) cc_final: 0.7574 (mp0) outliers start: 42 outliers final: 32 residues processed: 349 average time/residue: 0.0846 time to fit residues: 45.9081 Evaluate side-chains 331 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 298 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 479 HIS Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 787 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 45 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN D 150 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.119554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.103127 restraints weight = 32610.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.105872 restraints weight = 15657.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.107636 restraints weight = 9327.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.108817 restraints weight = 6485.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.109544 restraints weight = 5037.160| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 1.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 14135 Z= 0.229 Angle : 0.907 11.563 19221 Z= 0.453 Chirality : 0.051 0.280 2252 Planarity : 0.005 0.055 2397 Dihedral : 5.605 57.972 1912 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.09 % Allowed : 23.83 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.20), residues: 1734 helix: 0.53 (0.15), residues: 1072 sheet: None (None), residues: 0 loop : -3.06 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 157 TYR 0.035 0.002 TYR C 397 PHE 0.064 0.003 PHE A 200 TRP 0.024 0.003 TRP B 166 HIS 0.009 0.002 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (14114) covalent geometry : angle 0.90383 / 0.45 (19185) SS BOND : bond 0.01287 / 0.99 ( 12) SS BOND : angle 1.74532 / 1.25 ( 24) hydrogen bonds : bond 0.05313 / 3.48 ( 758) hydrogen bonds : angle 4.62615 / 3.26 ( 2235) Misc. bond : bond 0.00257 / 0.15 ( 5) link_BETA1-4 : bond 0.00840 / 0.43 ( 2) link_BETA1-4 : angle 2.55326 / 1.12 ( 6) link_NAG-ASN : bond 0.00748 / 0.39 ( 2) link_NAG-ASN : angle 2.39148 / 1.27 ( 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 391 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 330 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8394 (mm-40) REVERT: A 152 MET cc_start: 0.8376 (tpp) cc_final: 0.8113 (tpp) REVERT: A 153 GLN cc_start: 0.7850 (tp-100) cc_final: 0.7278 (pt0) REVERT: A 167 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8301 (mp10) REVERT: A 262 MET cc_start: 0.8340 (mmm) cc_final: 0.7969 (mmm) REVERT: A 286 ILE cc_start: 0.7114 (mm) cc_final: 0.6907 (tp) REVERT: B 107 ARG cc_start: 0.7392 (mmm160) cc_final: 0.7152 (mmm160) REVERT: C 160 LYS cc_start: 0.8983 (tttt) cc_final: 0.8651 (tmtt) REVERT: C 250 MET cc_start: 0.8292 (mmm) cc_final: 0.8059 (mtp) REVERT: C 282 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7927 (t0) REVERT: C 409 ARG cc_start: 0.7098 (tpt90) cc_final: 0.6589 (mtp-110) REVERT: C 413 GLN cc_start: 0.8733 (mt0) cc_final: 0.8062 (mp10) REVERT: C 426 THR cc_start: 0.8932 (m) cc_final: 0.8693 (t) REVERT: C 446 MET cc_start: 0.7713 (pmm) cc_final: 0.6327 (mtp) REVERT: C 451 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: C 462 MET cc_start: 0.7845 (tpp) cc_final: 0.7605 (mmm) REVERT: C 555 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8601 (tp-100) REVERT: C 572 GLU cc_start: 0.7746 (tt0) cc_final: 0.7482 (pt0) REVERT: C 756 ARG cc_start: 0.8281 (tpt90) cc_final: 0.7633 (tpt90) REVERT: D 208 GLN cc_start: 0.8453 (mp10) cc_final: 0.7916 (mp10) REVERT: D 332 MET cc_start: 0.7920 (mtp) cc_final: 0.7709 (mtp) REVERT: D 400 THR cc_start: 0.9264 (p) cc_final: 0.8964 (t) REVERT: D 739 GLU cc_start: 0.8034 (mp0) cc_final: 0.7599 (mp0) outliers start: 61 outliers final: 32 residues processed: 370 average time/residue: 0.0903 time to fit residues: 51.5908 Evaluate side-chains 319 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 285 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain C residue 479 HIS Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain D residue 100 ASP 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 298 SER Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 787 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 62 optimal weight: 0.9980 chunk 88 optimal weight: 0.0870 chunk 169 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 GLN A 195 HIS B 153 GLN ** C 214 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 = 0.3809 r_free = 0.3809 target = 0.123220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.106003 restraints weight = 33252.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.108887 restraints weight = 15812.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.110765 restraints weight = 9426.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.112017 restraints weight = 6514.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.112748 restraints weight = 5084.207| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 1.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14135 Z= 0.148 Angle : 0.827 12.162 19221 Z= 0.400 Chirality : 0.047 0.282 2252 Planarity : 0.004 0.054 2397 Dihedral : 5.216 49.115 1912 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.42 % Allowed : 27.79 % Favored : 69.80 % 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: -0.74 (0.20), residues: 1734 helix: 0.85 (0.16), residues: 1073 sheet: None (None), residues: 0 loop : -2.90 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 756 TYR 0.026 0.002 TYR C 397 PHE 0.042 0.002 PHE D 329 TRP 0.039 0.002 TRP B 166 HIS 0.007 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (14114) covalent geometry : angle 0.82244 / 0.40 (19185) SS BOND : bond 0.00353 / 0.26 ( 12) SS BOND : angle 2.13879 / 1.69 ( 24) hydrogen bonds : bond 0.04326 / 2.82 ( 758) hydrogen bonds : angle 4.34694 / 3.06 ( 2235) Misc. bond : bond 0.00236 / 0.12 ( 5) link_BETA1-4 : bond 0.01190 / 0.62 ( 2) link_BETA1-4 : angle 1.93362 / 0.93 ( 6) link_NAG-ASN : bond 0.00796 / 0.42 ( 2) link_NAG-ASN : angle 2.23724 / 1.12 ( 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 351 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 315 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8449 (mm110) REVERT: A 125 LYS cc_start: 0.8673 (mmtt) cc_final: 0.8422 (mmtt) REVERT: A 153 GLN cc_start: 0.7655 (tp-100) cc_final: 0.7381 (pt0) REVERT: A 201 GLU cc_start: 0.5633 (tp30) cc_final: 0.4953 (mt-10) REVERT: A 262 MET cc_start: 0.8250 (mmm) cc_final: 0.8012 (mmm) REVERT: B 107 ARG cc_start: 0.7311 (mmm160) cc_final: 0.6998 (mmm160) REVERT: B 262 MET cc_start: 0.7830 (tpp) cc_final: 0.7229 (tpp) REVERT: B 292 ILE cc_start: 0.8846 (mt) cc_final: 0.8468 (tp) REVERT: C 160 LYS cc_start: 0.8992 (tttt) cc_final: 0.8634 (tmmt) REVERT: C 191 SER cc_start: 0.8476 (t) cc_final: 0.8273 (p) REVERT: C 206 ILE cc_start: 0.9226 (mp) cc_final: 0.8886 (mt) REVERT: C 413 GLN cc_start: 0.8684 (mt0) cc_final: 0.8040 (mp10) REVERT: C 446 MET cc_start: 0.7529 (pmm) cc_final: 0.6265 (mtp) REVERT: C 497 TYR cc_start: 0.8654 (t80) cc_final: 0.8371 (t80) REVERT: C 547 TYR cc_start: 0.8095 (m-80) cc_final: 0.7806 (m-80) REVERT: C 555 GLN cc_start: 0.8847 (tp-100) cc_final: 0.8553 (tp-100) REVERT: C 622 SER cc_start: 0.6252 (m) cc_final: 0.5745 (p) REVERT: C 756 ARG cc_start: 0.8199 (tpt90) cc_final: 0.7474 (tpt90) REVERT: C 767 ARG cc_start: 0.5416 (ptm160) cc_final: 0.4651 (ptt180) REVERT: D 208 GLN cc_start: 0.8370 (mp10) cc_final: 0.8132 (mp10) REVERT: D 400 THR cc_start: 0.9293 (p) cc_final: 0.9022 (t) REVERT: D 416 GLU cc_start: 0.8931 (tp30) cc_final: 0.8555 (tp30) REVERT: D 599 GLU cc_start: 0.7191 (pt0) cc_final: 0.6986 (pt0) REVERT: D 739 GLU cc_start: 0.7989 (mp0) cc_final: 0.7608 (mp0) outliers start: 36 outliers final: 26 residues processed: 341 average time/residue: 0.0888 time to fit residues: 47.0146 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 : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 479 HIS Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 519 LEU 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 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 298 SER Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 438 CYS Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 661 PHE Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 787 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 154 optimal weight: 0.0870 chunk 9 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 138 optimal weight: 0.0870 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 ASN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.122084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104926 restraints weight = 33251.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.107779 restraints weight = 15876.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.109609 restraints weight = 9504.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.110827 restraints weight = 6647.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.111588 restraints weight = 5189.846| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 1.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14135 Z= 0.156 Angle : 0.835 18.888 19221 Z= 0.402 Chirality : 0.047 0.321 2252 Planarity : 0.004 0.053 2397 Dihedral : 5.086 45.229 1912 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.01 % Allowed : 28.59 % Favored : 69.40 % 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: -0.55 (0.20), residues: 1734 helix: 1.03 (0.16), residues: 1071 sheet: None (None), residues: 0 loop : -2.85 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 756 TYR 0.029 0.001 TYR C 397 PHE 0.043 0.002 PHE A 119 TRP 0.021 0.002 TRP D 524 HIS 0.007 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (14114) covalent geometry : angle 0.83141 / 0.40 (19185) SS BOND : bond 0.00342 / 0.21 ( 12) SS BOND : angle 2.08598 / 1.57 ( 24) hydrogen bonds : bond 0.04287 / 2.82 ( 758) hydrogen bonds : angle 4.35670 / 3.06 ( 2235) Misc. bond : bond 0.00230 / 0.12 ( 5) link_BETA1-4 : bond 0.01007 / 0.52 ( 2) link_BETA1-4 : angle 1.76838 / 0.82 ( 6) link_NAG-ASN : bond 0.00666 / 0.35 ( 2) link_NAG-ASN : angle 2.20865 / 1.10 ( 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 338 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 308 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5997 (mm) REVERT: A 125 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8431 (mmtt) REVERT: A 151 ARG cc_start: 0.8102 (ptm-80) cc_final: 0.7678 (ptt90) REVERT: A 201 GLU cc_start: 0.5772 (tp30) cc_final: 0.5182 (mt-10) REVERT: B 107 ARG cc_start: 0.7261 (mmm160) cc_final: 0.7059 (mmm160) REVERT: B 262 MET cc_start: 0.7670 (tpp) cc_final: 0.7121 (tpp) REVERT: B 283 VAL cc_start: 0.8879 (m) cc_final: 0.8648 (t) REVERT: B 292 ILE cc_start: 0.8887 (mt) cc_final: 0.8507 (tp) REVERT: C 206 ILE cc_start: 0.9245 (mp) cc_final: 0.8971 (mt) REVERT: C 250 MET cc_start: 0.8062 (tpp) cc_final: 0.7818 (mtp) REVERT: C 413 GLN cc_start: 0.8718 (mt0) cc_final: 0.8073 (mp10) REVERT: C 446 MET cc_start: 0.7581 (pmm) cc_final: 0.6327 (mtp) REVERT: C 497 TYR cc_start: 0.8642 (t80) cc_final: 0.8432 (t80) REVERT: C 547 TYR cc_start: 0.8145 (m-80) cc_final: 0.7918 (m-80) REVERT: C 555 GLN cc_start: 0.8861 (tp-100) cc_final: 0.8566 (tp-100) REVERT: C 622 SER cc_start: 0.6389 (m) cc_final: 0.5662 (p) REVERT: C 756 ARG cc_start: 0.8209 (tpt90) cc_final: 0.7481 (tpt90) REVERT: D 208 GLN cc_start: 0.8438 (mp10) cc_final: 0.8213 (mp10) REVERT: D 400 THR cc_start: 0.9313 (p) cc_final: 0.9066 (t) REVERT: D 602 TYR cc_start: 0.8315 (m-10) cc_final: 0.8056 (m-80) REVERT: D 739 GLU cc_start: 0.7962 (mp0) cc_final: 0.7692 (mp0) outliers start: 30 outliers final: 23 residues processed: 332 average time/residue: 0.0858 time to fit residues: 43.9047 Evaluate side-chains 307 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 283 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 479 HIS Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 438 CYS Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 661 PHE Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 787 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 66 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN C 468 ASN D 479 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.122215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.105117 restraints weight = 33410.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.107945 restraints weight = 15937.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.109763 restraints weight = 9539.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.110946 restraints weight = 6673.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.111729 restraints weight = 5222.881| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 1.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14135 Z= 0.156 Angle : 0.828 11.306 19221 Z= 0.399 Chirality : 0.047 0.328 2252 Planarity : 0.004 0.052 2397 Dihedral : 5.033 40.452 1912 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.81 % Allowed : 29.66 % Favored : 68.52 % 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: -0.51 (0.20), residues: 1734 helix: 1.07 (0.16), residues: 1071 sheet: None (None), residues: 0 loop : -2.85 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 756 TYR 0.035 0.002 TYR C 459 PHE 0.056 0.002 PHE D 329 TRP 0.021 0.002 TRP D 524 HIS 0.007 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (14114) covalent geometry : angle 0.82449 / 0.40 (19185) SS BOND : bond 0.00269 / 0.17 ( 12) SS BOND : angle 1.77862 / 1.30 ( 24) hydrogen bonds : bond 0.04254 / 2.81 ( 758) hydrogen bonds : angle 4.30502 / 3.03 ( 2235) Misc. bond : bond 0.00219 / 0.11 ( 5) link_BETA1-4 : bond 0.00831 / 0.43 ( 2) link_BETA1-4 : angle 1.75881 / 0.80 ( 6) link_NAG-ASN : bond 0.00613 / 0.32 ( 2) link_NAG-ASN : angle 2.21629 / 1.10 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2106.07 seconds wall clock time: 37 minutes 7.48 seconds (2227.48 seconds total)