Starting phenix.real_space_refine on Thu Jul 31 23:51:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cq7_30438/07_2025/7cq7_30438.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cq7_30438/07_2025/7cq7_30438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cq7_30438/07_2025/7cq7_30438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cq7_30438/07_2025/7cq7_30438.map" model { file = "/net/cci-nas-00/data/ceres_data/7cq7_30438/07_2025/7cq7_30438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cq7_30438/07_2025/7cq7_30438.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 2, 'ASN:plan1': 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: {'GLU:plan': 2, 'ASN:plan1': 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: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} 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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CL': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CL': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.07, per 1000 atoms: 0.66 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: 3.75 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.42 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: 4.23 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4350 1.34 - 1.47: 3464 1.47 - 1.59: 6154 1.59 - 1.71: 6 1.71 - 1.83: 140 Bond restraints: 14114 Sorted by residual: bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C5 ADP D 901 " pdb=" C6 ADP D 901 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 ADP C 901 " pdb=" C6 ADP C 901 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" CB VAL C 586 " pdb=" CG1 VAL C 586 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.49e+00 ... (remaining 14109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 18276 2.18 - 4.36: 742 4.36 - 6.54: 109 6.54 - 8.72: 43 8.72 - 10.90: 15 Bond angle restraints: 19185 Sorted by residual: angle pdb=" C THR A 282 " pdb=" N VAL A 283 " pdb=" CA VAL A 283 " ideal model delta sigma weight residual 120.24 125.32 -5.08 6.30e-01 2.52e+00 6.50e+01 angle pdb=" N GLN D 722 " pdb=" CA GLN D 722 " pdb=" C GLN D 722 " ideal model delta sigma weight residual 114.75 105.85 8.90 1.26e+00 6.30e-01 4.99e+01 angle pdb=" C ARG B 271 " pdb=" N THR B 272 " pdb=" CA THR B 272 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C ARG A 271 " pdb=" N THR A 272 " pdb=" CA THR A 272 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.49e+01 angle pdb=" N ILE D 724 " pdb=" CA ILE D 724 " pdb=" C ILE D 724 " ideal model delta sigma weight residual 110.62 115.92 -5.30 1.14e+00 7.69e-01 2.16e+01 ... (remaining 19180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 8213 22.84 - 45.68: 182 45.68 - 68.52: 10 68.52 - 91.36: 8 91.36 - 114.20: 1 Dihedral angle restraints: 8414 sinusoidal: 3299 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASP C 282 " pdb=" C ASP C 282 " pdb=" N THR C 283 " pdb=" CA THR C 283 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" C5' ADP D 901 " pdb=" O5' ADP D 901 " pdb=" PA ADP D 901 " pdb=" O2A ADP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 -174.20 114.20 1 2.00e+01 2.50e-03 3.38e+01 dihedral pdb=" CA ARG A 107 " pdb=" C ARG A 107 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " ideal model delta harmonic sigma weight residual 180.00 152.58 27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 8411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1658 0.060 - 0.120: 513 0.120 - 0.180: 68 0.180 - 0.240: 11 0.240 - 0.301: 2 Chirality restraints: 2252 Sorted by residual: chirality pdb=" CB ILE D 721 " pdb=" CA ILE D 721 " pdb=" CG1 ILE D 721 " pdb=" CG2 ILE D 721 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE C 724 " pdb=" CA ILE C 724 " pdb=" CG1 ILE C 724 " pdb=" CG2 ILE C 724 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB ILE D 275 " pdb=" CA ILE D 275 " pdb=" CG1 ILE D 275 " pdb=" CG2 ILE D 275 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2249 not shown) Planarity restraints: 2399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 179 " 0.028 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP C 179 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP C 179 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 179 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 179 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 179 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 179 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 179 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 179 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 179 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 783 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C THR C 783 " 0.048 2.00e-02 2.50e+03 pdb=" O THR C 783 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG C 784 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 349 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C MET D 349 " -0.044 2.00e-02 2.50e+03 pdb=" O MET D 349 " 0.016 2.00e-02 2.50e+03 pdb=" N TRP D 350 " 0.015 2.00e-02 2.50e+03 ... (remaining 2396 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 75 2.51 - 3.11: 10133 3.11 - 3.71: 21215 3.71 - 4.30: 29202 4.30 - 4.90: 49468 Nonbonded interactions: 110093 Sorted by model distance: nonbonded pdb=" OD2 ASP D 786 " pdb=" O2' ADP D 901 " model vdw 1.915 3.040 nonbonded pdb=" O MET C 368 " pdb=" OH TYR C 579 " model vdw 2.236 3.040 nonbonded pdb=" CG HIS C 658 " pdb=" N7 ADP C 901 " model vdw 2.251 2.672 nonbonded pdb=" O MET D 368 " pdb=" OH TYR D 579 " model vdw 2.261 3.040 nonbonded pdb=" NH2 ARG D 767 " pdb=" O2B ADP D 901 " model vdw 2.261 3.120 ... (remaining 110088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 73 through 306) selection = (chain 'B' and (resid 73 through 130 or resid 142 through 245 or resid 253 throu \ gh 306)) } ncs_group { reference = (chain 'C' and (resid 94 through 115 or (resid 116 and (name N or name CA or nam \ e C or name O or name CB )) or resid 121 through 652 or (resid 653 through 656 a \ nd (name N or name CA or name C or name O or name CB )) or resid 657 through 664 \ or resid 673 through 693 or resid 706 through 789 or (resid 790 and (name N or \ name CA or name C or name O or name CB )) or resid 901 through 902)) selection = (chain 'D' and (resid 94 through 116 or resid 121 through 366 or (resid 367 and \ (name N or name CA or name C or name O or name CB )) or resid 368 through 619 or \ (resid 620 and (name N or name CA or name C or name O or name CB )) or resid 62 \ 1 through 642 or (resid 643 and (name N or name CA or name C or name O or name C \ B )) or resid 644 through 690 or (resid 691 and (name N or name CA or name C or \ name O or name CB )) or resid 692 or (resid 693 and (name N or name CA or name C \ or name O or name CB )) or resid 706 through 707 or (resid 708 and (name N or n \ ame CA or name C or name O or name CB )) or resid 709 through 716 or (resid 717 \ and (name N or name CA or name C or name O or name CB )) or resid 718 or (resid \ 719 and (name N or name CA or name C or name O or name CB )) or resid 720 throug \ h 724 or (resid 725 through 732 and (name N or name CA or name C or name O or na \ me CB )) or resid 733 through 790 or resid 901 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: 1.550 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 34.720 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4342 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.641 14135 Z= 0.697 Angle : 1.074 10.899 19221 Z= 0.571 Chirality : 0.056 0.301 2252 Planarity : 0.008 0.063 2397 Dihedral : 10.352 114.200 5066 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.062 0.004 TRP C 179 HIS 0.020 0.002 HIS D 725 PHE 0.031 0.003 PHE D 279 TYR 0.022 0.002 TYR D 370 ARG 0.011 0.001 ARG D 326 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 2) link_NAG-ASN : angle 3.75561 ( 6) link_BETA1-4 : bond 0.00595 ( 2) link_BETA1-4 : angle 2.74501 ( 6) hydrogen bonds : bond 0.20482 ( 758) hydrogen bonds : angle 7.64867 ( 2235) SS BOND : bond 0.00331 ( 12) SS BOND : angle 1.82474 ( 24) covalent geometry : bond 0.00804 (14114) covalent geometry : angle 1.06949 (19185) Misc. bond : bond 0.32045 ( 5) *********************** 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 : 1.444 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: 0.4732 (m) REVERT: C 588 MET cc_start: 0.4373 (mtp) cc_final: 0.4139 (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: 0.2675 time to fit residues: 178.1529 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 : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 158 optimal weight: 0.0050 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN A 202 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 173 ASN C 183 ASN C 220 HIS C 468 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.129607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.113857 restraints weight = 31510.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.116990 restraints weight = 14601.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.119000 restraints weight = 8390.284| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5174 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14135 Z= 0.174 Angle : 0.834 10.545 19221 Z= 0.414 Chirality : 0.045 0.270 2252 Planarity : 0.006 0.048 2397 Dihedral : 6.697 108.307 1996 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.22 % Allowed : 11.61 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.19), residues: 1734 helix: -0.44 (0.15), residues: 1068 sheet: None (None), residues: 0 loop : -3.53 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 179 HIS 0.010 0.001 HIS C 658 PHE 0.036 0.002 PHE A 294 TYR 0.021 0.002 TYR C 547 ARG 0.007 0.001 ARG D 526 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 2) link_NAG-ASN : angle 3.40366 ( 6) link_BETA1-4 : bond 0.01189 ( 2) link_BETA1-4 : angle 1.91147 ( 6) hydrogen bonds : bond 0.04883 ( 758) hydrogen bonds : angle 4.62248 ( 2235) SS BOND : bond 0.00858 ( 12) SS BOND : angle 2.16001 ( 24) covalent geometry : bond 0.00378 (14114) covalent geometry : angle 0.82876 (19185) Misc. bond : bond 0.00155 ( 5) *********************** 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 339 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 291 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7290 (tpp) cc_final: 0.5580 (tpp) REVERT: A 168 GLU cc_start: 0.6482 (tm-30) cc_final: 0.6142 (tm-30) REVERT: B 192 LEU cc_start: 0.8471 (tp) cc_final: 0.7791 (mp) REVERT: B 281 ASP cc_start: 0.6946 (p0) cc_final: 0.6641 (p0) REVERT: C 323 LEU cc_start: 0.4610 (OUTLIER) cc_final: 0.3590 (mt) REVERT: C 570 MET cc_start: 0.5702 (mmp) cc_final: 0.5487 (mmp) REVERT: C 588 MET cc_start: 0.5501 (mtp) cc_final: 0.4794 (ppp) REVERT: C 589 THR cc_start: 0.6289 (m) cc_final: 0.5934 (m) REVERT: C 599 GLU cc_start: 0.4750 (OUTLIER) cc_final: 0.3551 (pm20) REVERT: C 659 ASN cc_start: 0.4079 (m-40) cc_final: 0.3087 (m110) REVERT: D 132 LEU cc_start: 0.7651 (mt) cc_final: 0.7395 (mt) REVERT: D 143 PHE cc_start: 0.7661 (t80) cc_final: 0.5968 (m-10) outliers start: 48 outliers final: 20 residues processed: 320 average time/residue: 0.3270 time to fit residues: 163.1084 Evaluate side-chains 252 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 3.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 193 PHE 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 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 646 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 83 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 102 optimal weight: 0.0030 chunk 25 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN ** B 113 GLN ** 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 396 ASN D 623 HIS ** D 768 HIS ** 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 = 0.3858 r_free = 0.3858 target = 0.129096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.112691 restraints weight = 31652.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.115992 restraints weight = 14479.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.118110 restraints weight = 8210.252| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5662 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14135 Z= 0.180 Angle : 0.793 12.095 19221 Z= 0.390 Chirality : 0.046 0.339 2252 Planarity : 0.005 0.043 2397 Dihedral : 6.117 86.707 1996 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.23 % Allowed : 13.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.19), residues: 1734 helix: 0.23 (0.16), residues: 1069 sheet: None (None), residues: 0 loop : -3.16 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 166 HIS 0.013 0.001 HIS C 658 PHE 0.035 0.002 PHE A 294 TYR 0.020 0.002 TYR D 579 ARG 0.006 0.001 ARG B 131 Details of bonding type rmsd link_NAG-ASN : bond 0.01756 ( 2) link_NAG-ASN : angle 2.31914 ( 6) link_BETA1-4 : bond 0.00552 ( 2) link_BETA1-4 : angle 1.40182 ( 6) hydrogen bonds : bond 0.04549 ( 758) hydrogen bonds : angle 4.36747 ( 2235) SS BOND : bond 0.00999 ( 12) SS BOND : angle 1.35407 ( 24) covalent geometry : bond 0.00396 (14114) covalent geometry : angle 0.79048 (19185) Misc. bond : bond 0.00352 ( 5) *********************** 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 347 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 284 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6875 (p0) REVERT: A 152 MET cc_start: 0.7383 (tpp) cc_final: 0.5765 (tpp) REVERT: A 168 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6844 (tm-30) REVERT: A 228 TYR cc_start: 0.5685 (t80) cc_final: 0.5388 (t80) REVERT: B 152 MET cc_start: 0.5698 (ptm) cc_final: 0.5333 (ptm) REVERT: B 192 LEU cc_start: 0.8040 (tp) cc_final: 0.7588 (mp) REVERT: B 281 ASP cc_start: 0.7149 (p0) cc_final: 0.6671 (p0) REVERT: C 160 LYS cc_start: 0.4982 (ttpt) cc_final: 0.4354 (mtpt) REVERT: C 366 GLU cc_start: 0.6677 (mp0) cc_final: 0.6431 (mp0) REVERT: C 566 LEU cc_start: 0.7598 (mt) cc_final: 0.7387 (mt) REVERT: C 599 GLU cc_start: 0.5488 (OUTLIER) cc_final: 0.4545 (pm20) REVERT: D 132 LEU cc_start: 0.8078 (mt) cc_final: 0.7797 (mt) REVERT: D 143 PHE cc_start: 0.7795 (t80) cc_final: 0.5869 (m-10) REVERT: D 407 ILE cc_start: 0.6429 (mp) cc_final: 0.5870 (mm) REVERT: D 615 HIS cc_start: 0.6041 (t-90) cc_final: 0.5372 (t-90) REVERT: D 741 MET cc_start: 0.7524 (ppp) cc_final: 0.7179 (tmm) REVERT: D 766 LEU cc_start: 0.3682 (mt) cc_final: 0.2312 (mp) outliers start: 63 outliers final: 25 residues processed: 319 average time/residue: 0.2179 time to fit residues: 106.9631 Evaluate side-chains 264 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 193 PHE 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 250 MET Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 496 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 D residue 140 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 646 VAL 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 89 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 50 optimal weight: 0.4980 chunk 127 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 101 optimal weight: 0.0060 chunk 135 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN C 659 ASN C 683 GLN ** D 183 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.130063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.113687 restraints weight = 31473.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.117016 restraints weight = 14295.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.119125 restraints weight = 8146.706| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5827 moved from start: 0.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 14135 Z= 0.145 Angle : 0.731 9.634 19221 Z= 0.362 Chirality : 0.044 0.224 2252 Planarity : 0.004 0.043 2397 Dihedral : 5.632 68.962 1996 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.89 % Allowed : 15.57 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1734 helix: 0.61 (0.16), residues: 1074 sheet: None (None), residues: 0 loop : -3.05 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 325 HIS 0.009 0.001 HIS C 658 PHE 0.028 0.002 PHE B 91 TYR 0.017 0.001 TYR D 99 ARG 0.011 0.000 ARG D 362 Details of bonding type rmsd link_NAG-ASN : bond 0.01041 ( 2) link_NAG-ASN : angle 2.33691 ( 6) link_BETA1-4 : bond 0.01107 ( 2) link_BETA1-4 : angle 2.50432 ( 6) hydrogen bonds : bond 0.04030 ( 758) hydrogen bonds : angle 4.11966 ( 2235) SS BOND : bond 0.00372 ( 12) SS BOND : angle 0.97817 ( 24) covalent geometry : bond 0.00319 (14114) covalent geometry : angle 0.72792 (19185) Misc. bond : bond 0.00351 ( 5) *********************** 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 329 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 271 time to evaluate : 1.872 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: 0.7204 (OUTLIER) cc_final: 0.6893 (p0) REVERT: A 152 MET cc_start: 0.7403 (tpp) cc_final: 0.5689 (tpp) REVERT: A 168 GLU cc_start: 0.7236 (tm-30) cc_final: 0.7000 (tm-30) REVERT: A 228 TYR cc_start: 0.5638 (t80) cc_final: 0.5392 (t80) REVERT: A 229 LYS cc_start: 0.5767 (pttp) cc_final: 0.5455 (tmtt) REVERT: A 231 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7549 (mm) REVERT: B 152 MET cc_start: 0.5677 (ptm) cc_final: 0.5444 (ptm) REVERT: B 281 ASP cc_start: 0.7027 (p0) cc_final: 0.6518 (p0) REVERT: C 95 GLU cc_start: 0.5068 (mp0) cc_final: 0.4269 (tt0) REVERT: C 556 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.5815 (mt) REVERT: C 570 MET cc_start: 0.7344 (mmm) cc_final: 0.6078 (tpp) REVERT: C 599 GLU cc_start: 0.5674 (OUTLIER) cc_final: 0.4771 (pm20) REVERT: C 659 ASN cc_start: 0.4901 (OUTLIER) cc_final: 0.4671 (m-40) REVERT: D 301 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6716 (t80) REVERT: D 407 ILE cc_start: 0.6504 (mp) cc_final: 0.6234 (mt) REVERT: D 606 ILE cc_start: 0.6057 (OUTLIER) cc_final: 0.5757 (mt) REVERT: D 740 PHE cc_start: 0.7836 (m-80) cc_final: 0.7611 (m-80) REVERT: D 741 MET cc_start: 0.7259 (ppp) cc_final: 0.6779 (tmm) REVERT: D 766 LEU cc_start: 0.3729 (OUTLIER) cc_final: 0.2329 (mp) outliers start: 58 outliers final: 31 residues processed: 303 average time/residue: 0.2749 time to fit residues: 129.7135 Evaluate side-chains 288 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 249 time to evaluate : 3.044 ------------------------------------------------------------------------------- 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 142 CYS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 433 TYR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 659 ASN 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 188 LEU Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 606 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 141 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 73 optimal weight: 0.0040 chunk 41 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 HIS B 203 ASN C 393 ASN C 576 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN D 396 ASN D 605 HIS D 623 HIS D 768 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.128781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.112246 restraints weight = 32037.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.115444 restraints weight = 15125.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.117522 restraints weight = 8836.441| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.8069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14135 Z= 0.196 Angle : 0.822 19.271 19221 Z= 0.404 Chirality : 0.048 0.507 2252 Planarity : 0.005 0.098 2397 Dihedral : 5.770 54.437 1996 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.36 % Allowed : 15.50 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.20), residues: 1734 helix: 0.66 (0.16), residues: 1081 sheet: -3.11 (3.26), residues: 5 loop : -3.01 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 541 HIS 0.035 0.002 HIS C 658 PHE 0.036 0.002 PHE A 193 TYR 0.020 0.002 TYR C 345 ARG 0.011 0.001 ARG A 107 Details of bonding type rmsd link_NAG-ASN : bond 0.02058 ( 2) link_NAG-ASN : angle 2.50506 ( 6) link_BETA1-4 : bond 0.00348 ( 2) link_BETA1-4 : angle 1.62688 ( 6) hydrogen bonds : bond 0.04306 ( 758) hydrogen bonds : angle 4.13808 ( 2235) SS BOND : bond 0.00391 ( 12) SS BOND : angle 1.13235 ( 24) covalent geometry : bond 0.00427 (14114) covalent geometry : angle 0.81965 (19185) Misc. bond : bond 0.00432 ( 5) *********************** 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 391 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 326 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7809 (tpp) cc_final: 0.6447 (tpp) REVERT: A 168 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7395 (tm-30) REVERT: A 228 TYR cc_start: 0.6308 (t80) cc_final: 0.5983 (t80) REVERT: A 229 LYS cc_start: 0.5993 (pttp) cc_final: 0.5639 (tmtt) REVERT: B 281 ASP cc_start: 0.7159 (p0) cc_final: 0.6587 (p0) REVERT: C 95 GLU cc_start: 0.5556 (mp0) cc_final: 0.4977 (tt0) REVERT: C 433 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.6363 (m-80) REVERT: C 505 TYR cc_start: 0.7807 (t80) cc_final: 0.7300 (t80) REVERT: C 556 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6819 (mt) REVERT: C 566 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8102 (tt) REVERT: C 599 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.5827 (pm20) REVERT: D 398 TRP cc_start: 0.7547 (m100) cc_final: 0.7197 (m-10) REVERT: D 503 TRP cc_start: 0.7031 (t60) cc_final: 0.6417 (t60) REVERT: D 756 ARG cc_start: 0.7166 (mmp80) cc_final: 0.6236 (mtt180) outliers start: 65 outliers final: 31 residues processed: 362 average time/residue: 0.2919 time to fit residues: 164.0005 Evaluate side-chains 306 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 127 TRP 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 229 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 433 TYR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 566 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 C residue 779 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 787 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 59 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 162 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN D 555 GLN D 623 HIS D 658 HIS ** D 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.134290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.118566 restraints weight = 32677.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.121626 restraints weight = 15690.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.123583 restraints weight = 9291.813| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.9413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14135 Z= 0.170 Angle : 0.791 12.776 19221 Z= 0.386 Chirality : 0.047 0.243 2252 Planarity : 0.004 0.046 2397 Dihedral : 5.631 54.086 1996 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.09 % Allowed : 18.86 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1734 helix: 0.79 (0.16), residues: 1077 sheet: -3.23 (3.26), residues: 5 loop : -2.88 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 524 HIS 0.006 0.001 HIS C 658 PHE 0.038 0.002 PHE C 328 TYR 0.022 0.002 TYR C 790 ARG 0.007 0.001 ARG B 107 Details of bonding type rmsd link_NAG-ASN : bond 0.00671 ( 2) link_NAG-ASN : angle 2.21870 ( 6) link_BETA1-4 : bond 0.01305 ( 2) link_BETA1-4 : angle 2.20756 ( 6) hydrogen bonds : bond 0.04070 ( 758) hydrogen bonds : angle 4.06260 ( 2235) SS BOND : bond 0.00411 ( 12) SS BOND : angle 1.10757 ( 24) covalent geometry : bond 0.00384 (14114) covalent geometry : angle 0.78919 (19185) Misc. bond : bond 0.00264 ( 5) *********************** 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 392 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 331 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7196 (p0) REVERT: A 152 MET cc_start: 0.8119 (tpp) cc_final: 0.6753 (tpp) REVERT: A 167 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7816 (mm-40) REVERT: A 229 LYS cc_start: 0.5965 (pttp) cc_final: 0.5727 (tmtt) REVERT: B 281 ASP cc_start: 0.7086 (p0) cc_final: 0.6573 (p0) REVERT: C 433 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6526 (m-80) REVERT: C 505 TYR cc_start: 0.7803 (t80) cc_final: 0.7039 (t80) REVERT: C 556 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7629 (mt) REVERT: C 599 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6255 (pm20) REVERT: C 640 ARG cc_start: 0.4981 (ttp80) cc_final: 0.4757 (ttt180) REVERT: D 398 TRP cc_start: 0.7715 (m100) cc_final: 0.7137 (m-10) REVERT: D 503 TRP cc_start: 0.7579 (t60) cc_final: 0.7188 (t60) REVERT: D 739 GLU cc_start: 0.7507 (mp0) cc_final: 0.7161 (mp0) REVERT: D 741 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7512 (tmm) REVERT: D 756 ARG cc_start: 0.7485 (mmp80) cc_final: 0.6817 (mtt180) outliers start: 61 outliers final: 34 residues processed: 363 average time/residue: 0.2345 time to fit residues: 131.0611 Evaluate side-chains 314 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 115 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 433 TYR Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 479 HIS Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 679 ILE 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 188 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 741 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 127 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN D 451 GLN D 768 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.132145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.115923 restraints weight = 33087.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.118973 restraints weight = 15492.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.120950 restraints weight = 9068.140| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 1.0240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14135 Z= 0.153 Angle : 0.784 16.035 19221 Z= 0.377 Chirality : 0.046 0.358 2252 Planarity : 0.004 0.047 2397 Dihedral : 5.621 49.001 1996 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.22 % Allowed : 21.74 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.20), residues: 1734 helix: 0.90 (0.16), residues: 1071 sheet: None (None), residues: 0 loop : -2.85 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 269 HIS 0.007 0.001 HIS C 658 PHE 0.032 0.002 PHE C 328 TYR 0.031 0.002 TYR C 397 ARG 0.009 0.001 ARG D 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00120 ( 2) link_NAG-ASN : angle 2.56829 ( 6) link_BETA1-4 : bond 0.00612 ( 2) link_BETA1-4 : angle 1.92018 ( 6) hydrogen bonds : bond 0.04074 ( 758) hydrogen bonds : angle 4.04672 ( 2235) SS BOND : bond 0.00325 ( 12) SS BOND : angle 1.15848 ( 24) covalent geometry : bond 0.00340 (14114) covalent geometry : angle 0.78136 (19185) Misc. bond : bond 0.00183 ( 5) *********************** 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 361 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 313 time to evaluate : 1.803 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: 0.7635 (OUTLIER) cc_final: 0.7081 (p0) REVERT: A 152 MET cc_start: 0.8150 (tpp) cc_final: 0.6931 (ttp) REVERT: A 167 GLN cc_start: 0.8226 (mm-40) cc_final: 0.8014 (mm-40) REVERT: A 228 TYR cc_start: 0.6136 (t80) cc_final: 0.5749 (t80) REVERT: B 281 ASP cc_start: 0.7152 (p0) cc_final: 0.6710 (p0) REVERT: C 157 ARG cc_start: 0.7756 (ttp80) cc_final: 0.7554 (ttp-110) REVERT: C 214 ASN cc_start: 0.7345 (m-40) cc_final: 0.6887 (m-40) REVERT: C 297 VAL cc_start: 0.8563 (t) cc_final: 0.8356 (m) REVERT: C 392 PHE cc_start: 0.7448 (t80) cc_final: 0.7242 (t80) REVERT: C 398 TRP cc_start: 0.5844 (OUTLIER) cc_final: 0.5275 (m-90) REVERT: C 433 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.6683 (m-80) REVERT: C 505 TYR cc_start: 0.7932 (t80) cc_final: 0.7059 (t80) REVERT: C 556 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7795 (mt) REVERT: C 599 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6472 (pm20) REVERT: D 109 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6480 (mp0) REVERT: D 486 ASN cc_start: 0.8085 (t0) cc_final: 0.7770 (t0) REVERT: D 497 TYR cc_start: 0.7904 (t80) cc_final: 0.7634 (t80) REVERT: D 570 MET cc_start: 0.7242 (ttp) cc_final: 0.6976 (mtp) REVERT: D 739 GLU cc_start: 0.7540 (mp0) cc_final: 0.7159 (mp0) REVERT: D 756 ARG cc_start: 0.7304 (mmp80) cc_final: 0.7022 (mtt180) REVERT: D 768 HIS cc_start: 0.7907 (OUTLIER) cc_final: 0.7690 (m-70) outliers start: 48 outliers final: 29 residues processed: 338 average time/residue: 0.2863 time to fit residues: 150.4782 Evaluate side-chains 320 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 285 time to evaluate : 2.653 ------------------------------------------------------------------------------- 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 115 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 398 TRP Chi-restraints excluded: chain C residue 433 TYR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 479 HIS Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 604 MET 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 100 ASP Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 571 MET Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 21 optimal weight: 0.2980 chunk 69 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN D 768 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.132620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.116116 restraints weight = 32929.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.119206 restraints weight = 15495.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.121213 restraints weight = 9077.883| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 1.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14135 Z= 0.141 Angle : 0.783 14.617 19221 Z= 0.374 Chirality : 0.045 0.207 2252 Planarity : 0.004 0.047 2397 Dihedral : 5.361 43.512 1996 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.68 % Allowed : 23.62 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.20), residues: 1734 helix: 1.03 (0.16), residues: 1072 sheet: None (None), residues: 0 loop : -2.78 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 524 HIS 0.044 0.001 HIS D 768 PHE 0.026 0.001 PHE A 193 TYR 0.030 0.001 TYR C 397 ARG 0.020 0.001 ARG D 767 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 2) link_NAG-ASN : angle 2.10562 ( 6) link_BETA1-4 : bond 0.00646 ( 2) link_BETA1-4 : angle 1.52730 ( 6) hydrogen bonds : bond 0.03994 ( 758) hydrogen bonds : angle 3.97337 ( 2235) SS BOND : bond 0.00248 ( 12) SS BOND : angle 1.04203 ( 24) covalent geometry : bond 0.00317 (14114) covalent geometry : angle 0.78127 (19185) Misc. bond : bond 0.00183 ( 5) *********************** 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 347 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 307 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7197 (p0) REVERT: A 152 MET cc_start: 0.8061 (tpp) cc_final: 0.6972 (ttp) REVERT: A 156 VAL cc_start: 0.8218 (t) cc_final: 0.7853 (p) REVERT: A 228 TYR cc_start: 0.6357 (t80) cc_final: 0.5909 (t80) REVERT: A 305 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7107 (tp) REVERT: B 281 ASP cc_start: 0.7227 (p0) cc_final: 0.6964 (p0) REVERT: C 214 ASN cc_start: 0.7336 (m-40) cc_final: 0.7082 (m-40) REVERT: C 305 VAL cc_start: 0.8961 (t) cc_final: 0.8691 (p) REVERT: C 413 GLN cc_start: 0.8495 (mt0) cc_final: 0.7611 (mp10) REVERT: C 433 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.6877 (m-80) REVERT: C 505 TYR cc_start: 0.7907 (t80) cc_final: 0.7102 (t80) REVERT: C 599 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6706 (pm20) REVERT: D 109 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6616 (mp0) REVERT: D 486 ASN cc_start: 0.7957 (t0) cc_final: 0.7694 (t0) REVERT: D 497 TYR cc_start: 0.8130 (t80) cc_final: 0.7902 (t80) REVERT: D 739 GLU cc_start: 0.7575 (mp0) cc_final: 0.7184 (mp0) outliers start: 40 outliers final: 26 residues processed: 335 average time/residue: 0.4132 time to fit residues: 218.5093 Evaluate side-chains 314 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 284 time to evaluate : 2.774 ------------------------------------------------------------------------------- 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 115 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 175 LEU 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 166 TRP Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 433 TYR Chi-restraints excluded: chain C residue 479 HIS Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 604 MET 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 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 630 VAL Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 646 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 38 optimal weight: 0.0050 chunk 72 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 42 optimal weight: 0.0070 chunk 102 optimal weight: 0.0970 chunk 155 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.2810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.133211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.117639 restraints weight = 31885.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.120601 restraints weight = 15023.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.122434 restraints weight = 8763.869| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 1.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 14135 Z= 0.138 Angle : 0.799 14.518 19221 Z= 0.378 Chirality : 0.044 0.216 2252 Planarity : 0.004 0.050 2397 Dihedral : 5.177 37.535 1996 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.48 % Allowed : 23.96 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.21), residues: 1734 helix: 1.05 (0.16), residues: 1073 sheet: None (None), residues: 0 loop : -2.64 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 179 HIS 0.005 0.001 HIS C 658 PHE 0.036 0.002 PHE A 119 TYR 0.034 0.001 TYR C 397 ARG 0.007 0.000 ARG D 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 2) link_NAG-ASN : angle 2.15107 ( 6) link_BETA1-4 : bond 0.00910 ( 2) link_BETA1-4 : angle 1.28464 ( 6) hydrogen bonds : bond 0.03862 ( 758) hydrogen bonds : angle 3.95819 ( 2235) SS BOND : bond 0.00322 ( 12) SS BOND : angle 1.09785 ( 24) covalent geometry : bond 0.00312 (14114) covalent geometry : angle 0.79729 (19185) Misc. bond : bond 0.00164 ( 5) *********************** 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 335 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 298 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7158 (p0) REVERT: A 97 GLU cc_start: 0.8294 (pt0) cc_final: 0.8000 (pt0) REVERT: A 228 TYR cc_start: 0.6389 (t80) cc_final: 0.6001 (t80) REVERT: B 107 ARG cc_start: 0.6447 (mmm160) cc_final: 0.6159 (mmm160) REVERT: B 262 MET cc_start: 0.6618 (tpp) cc_final: 0.6165 (tpp) REVERT: C 214 ASN cc_start: 0.7329 (m-40) cc_final: 0.6947 (m-40) REVERT: C 305 VAL cc_start: 0.8885 (t) cc_final: 0.8599 (p) REVERT: C 413 GLN cc_start: 0.8474 (mt0) cc_final: 0.7556 (mp10) REVERT: C 433 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.6941 (m-80) REVERT: C 505 TYR cc_start: 0.7834 (t80) cc_final: 0.6879 (t80) REVERT: C 599 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6564 (pm20) REVERT: C 767 ARG cc_start: 0.4756 (ptm160) cc_final: 0.4517 (ttt180) REVERT: D 109 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6597 (mp0) REVERT: D 308 VAL cc_start: 0.7245 (t) cc_final: 0.7002 (t) REVERT: D 497 TYR cc_start: 0.8150 (t80) cc_final: 0.7919 (t80) REVERT: D 739 GLU cc_start: 0.7584 (mp0) cc_final: 0.7201 (mp0) REVERT: D 756 ARG cc_start: 0.6853 (mtt180) cc_final: 0.6427 (ttm170) REVERT: D 783 THR cc_start: 0.8365 (m) cc_final: 0.8045 (t) outliers start: 37 outliers final: 24 residues processed: 322 average time/residue: 0.2319 time to fit residues: 116.7233 Evaluate side-chains 301 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 274 time to evaluate : 1.774 ------------------------------------------------------------------------------- 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 142 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 433 TYR Chi-restraints excluded: chain C residue 479 HIS Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 604 MET 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 100 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 THR 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 150 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 145 optimal weight: 0.5980 chunk 153 optimal weight: 0.0030 chunk 111 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 GLN D 676 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.133502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.116955 restraints weight = 32922.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.120040 restraints weight = 15617.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.122002 restraints weight = 9180.667| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 1.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14135 Z= 0.136 Angle : 0.792 14.035 19221 Z= 0.379 Chirality : 0.045 0.228 2252 Planarity : 0.004 0.050 2397 Dihedral : 5.050 33.385 1996 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.08 % Allowed : 25.17 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1734 helix: 1.15 (0.16), residues: 1073 sheet: None (None), residues: 0 loop : -2.59 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 524 HIS 0.005 0.001 HIS C 658 PHE 0.032 0.002 PHE A 119 TYR 0.033 0.001 TYR C 397 ARG 0.006 0.000 ARG D 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00052 ( 2) link_NAG-ASN : angle 2.10445 ( 6) link_BETA1-4 : bond 0.00673 ( 2) link_BETA1-4 : angle 1.06126 ( 6) hydrogen bonds : bond 0.03884 ( 758) hydrogen bonds : angle 4.01628 ( 2235) SS BOND : bond 0.00227 ( 12) SS BOND : angle 0.99852 ( 24) covalent geometry : bond 0.00306 (14114) covalent geometry : angle 0.79095 (19185) Misc. bond : bond 0.00162 ( 5) ********************** 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 340 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 309 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7671 (mt-10) REVERT: A 90 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7248 (p0) REVERT: A 97 GLU cc_start: 0.8374 (pt0) cc_final: 0.8136 (pt0) REVERT: A 228 TYR cc_start: 0.6436 (t80) cc_final: 0.6014 (t80) REVERT: B 107 ARG cc_start: 0.6459 (mmm160) cc_final: 0.6200 (mmm160) REVERT: B 241 MET cc_start: 0.7342 (ppp) cc_final: 0.7116 (ppp) REVERT: B 262 MET cc_start: 0.6707 (tpp) cc_final: 0.6245 (tpp) REVERT: C 214 ASN cc_start: 0.7387 (m-40) cc_final: 0.7030 (m-40) REVERT: C 413 GLN cc_start: 0.8556 (mt0) cc_final: 0.7689 (mp10) REVERT: C 433 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.7014 (m-80) REVERT: C 505 TYR cc_start: 0.7843 (t80) cc_final: 0.7071 (t80) REVERT: C 599 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6623 (pm20) REVERT: D 109 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6638 (mp0) REVERT: D 503 TRP cc_start: 0.7941 (t60) cc_final: 0.7158 (t60) REVERT: D 739 GLU cc_start: 0.7616 (mp0) cc_final: 0.7246 (mp0) REVERT: D 756 ARG cc_start: 0.7000 (mtt180) cc_final: 0.6529 (ttm170) outliers start: 31 outliers final: 23 residues processed: 327 average time/residue: 0.2278 time to fit residues: 115.5985 Evaluate side-chains 309 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 283 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 142 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 433 TYR Chi-restraints excluded: chain C residue 479 HIS Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 604 MET 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 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 420 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 630 VAL 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 29 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 chunk 162 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 153 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 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 = 0.3971 r_free = 0.3971 target = 0.133476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.116725 restraints weight = 33046.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.119854 restraints weight = 15634.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.121854 restraints weight = 9163.922| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 1.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14135 Z= 0.138 Angle : 0.792 13.636 19221 Z= 0.379 Chirality : 0.046 0.356 2252 Planarity : 0.004 0.043 2397 Dihedral : 4.941 37.557 1996 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.15 % Allowed : 25.97 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1734 helix: 1.13 (0.16), residues: 1074 sheet: None (None), residues: 0 loop : -2.53 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 524 HIS 0.006 0.001 HIS B 253 PHE 0.032 0.001 PHE A 119 TYR 0.032 0.001 TYR C 397 ARG 0.006 0.000 ARG D 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 2) link_NAG-ASN : angle 2.12489 ( 6) link_BETA1-4 : bond 0.00491 ( 2) link_BETA1-4 : angle 0.97198 ( 6) hydrogen bonds : bond 0.03942 ( 758) hydrogen bonds : angle 4.03802 ( 2235) SS BOND : bond 0.00249 ( 12) SS BOND : angle 1.08340 ( 24) covalent geometry : bond 0.00315 (14114) covalent geometry : angle 0.79071 (19185) Misc. bond : bond 0.00139 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5361.40 seconds wall clock time: 99 minutes 48.86 seconds (5988.86 seconds total)