Starting phenix.real_space_refine on Sun Sep 13 18:14:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5k7l_8215/09_2026/5k7l_8215.cif Found real_map, /net/cci-nas-00/data/ceres_data/5k7l_8215/09_2026/5k7l_8215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5k7l_8215/09_2026/5k7l_8215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5k7l_8215/09_2026/5k7l_8215.map" model { file = "/net/cci-nas-00/data/ceres_data/5k7l_8215/09_2026/5k7l_8215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5k7l_8215/09_2026/5k7l_8215.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5k7l_8215/09_2026/5k7l_8215.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5k7l_8215/09_2026/5k7l_8215.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 15972 2.51 5 N 4096 2.21 5 O 4500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.20s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24696 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5258 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 339 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 16, 'ARG:plan': 15, 'ASN:plan1': 5, 'ASP:plan': 11, 'GLN:plan1': 11, 'HIS:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 253 Chain: "B" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 881 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 9, 'ARG:plan': 5, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 142 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-1': 1, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 7 Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 6.25, per 1000 atoms: 0.25 Number of scatterers: 24696 At special positions: 0 Unit cell: (167.7, 167.7, 144.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 4500 8.00 N 4096 7.00 C 15972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 388 " " NAG C 901 " - " ASN C 388 " " NAG E 901 " - " ASN E 388 " " NAG G 901 " - " ASN G 388 " Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6400 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 16 sheets defined 63.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 17 through 26 removed outlier: 4.477A pdb=" N ASN A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.507A pdb=" N VAL A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.861A pdb=" N VAL A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.909A pdb=" N VAL A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 242 Proline residue: A 236 - end of helix removed outlier: 3.548A pdb=" N LYS A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 4.330A pdb=" N LEU A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 305 through 314 removed outlier: 3.672A pdb=" N PHE A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 326 removed outlier: 3.525A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 336 removed outlier: 3.542A pdb=" N LEU A 334 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 348 through 379 removed outlier: 3.922A pdb=" N LEU A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 removed outlier: 3.621A pdb=" N GLN A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 436 removed outlier: 3.920A pdb=" N TYR A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 499 removed outlier: 3.525A pdb=" N LEU A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 521 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.845A pdb=" N GLU A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 removed outlier: 3.649A pdb=" N GLU A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 625 removed outlier: 3.682A pdb=" N GLU A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 657 Processing helix chain 'A' and resid 657 through 668 removed outlier: 3.923A pdb=" N HIS A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 694 removed outlier: 3.791A pdb=" N MET A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 722 removed outlier: 4.235A pdb=" N VAL A 710 " --> pdb=" O PRO A 706 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 712 " --> pdb=" O HIS A 708 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 722 " --> pdb=" O ARG A 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.514A pdb=" N PHE B 16 " --> pdb=" O PHE B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 40 Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.526A pdb=" N LEU B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.745A pdb=" N THR B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 137 through 147 removed outlier: 3.873A pdb=" N MET B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 26 removed outlier: 4.477A pdb=" N ASN C 26 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.507A pdb=" N VAL C 60 " --> pdb=" O HIS C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 90 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 159 through 164 removed outlier: 3.861A pdb=" N VAL C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 194 removed outlier: 3.909A pdb=" N VAL C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 242 Proline residue: C 236 - end of helix removed outlier: 3.548A pdb=" N LYS C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 4.330A pdb=" N LEU C 251 " --> pdb=" O ASN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 305 through 314 removed outlier: 3.672A pdb=" N PHE C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN C 314 " --> pdb=" O ASN C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 326 removed outlier: 3.525A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 336 removed outlier: 3.542A pdb=" N LEU C 334 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'C' and resid 348 through 379 removed outlier: 3.922A pdb=" N LEU C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 400 removed outlier: 3.621A pdb=" N GLN C 394 " --> pdb=" O SER C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 436 removed outlier: 3.920A pdb=" N TYR C 423 " --> pdb=" O LYS C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 499 removed outlier: 3.525A pdb=" N LEU C 462 " --> pdb=" O MET C 458 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR C 485 " --> pdb=" O ASN C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 521 Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'C' and resid 533 through 545 Processing helix chain 'C' and resid 545 through 552 removed outlier: 3.845A pdb=" N GLU C 551 " --> pdb=" O LYS C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 570 removed outlier: 3.649A pdb=" N GLU C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 625 removed outlier: 3.682A pdb=" N GLU C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 657 Processing helix chain 'C' and resid 657 through 668 removed outlier: 3.923A pdb=" N HIS C 662 " --> pdb=" O THR C 658 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 694 removed outlier: 3.791A pdb=" N MET C 694 " --> pdb=" O GLU C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 722 removed outlier: 4.235A pdb=" N VAL C 710 " --> pdb=" O PRO C 706 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C 712 " --> pdb=" O HIS C 708 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU C 713 " --> pdb=" O PRO C 709 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 722 " --> pdb=" O ARG C 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.514A pdb=" N PHE D 16 " --> pdb=" O PHE D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 40 Processing helix chain 'D' and resid 44 through 56 removed outlier: 3.526A pdb=" N LEU D 48 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 77 removed outlier: 3.745A pdb=" N THR D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS D 77 " --> pdb=" O ALA D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 137 through 147 removed outlier: 3.873A pdb=" N MET D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET D 145 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 26 removed outlier: 4.477A pdb=" N ASN E 26 " --> pdb=" O VAL E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.507A pdb=" N VAL E 60 " --> pdb=" O HIS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 90 Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.861A pdb=" N VAL E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 194 removed outlier: 3.909A pdb=" N VAL E 178 " --> pdb=" O LYS E 174 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS E 180 " --> pdb=" O GLU E 176 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS E 181 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 187 " --> pdb=" O ARG E 183 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 242 Proline residue: E 236 - end of helix removed outlier: 3.548A pdb=" N LYS E 242 " --> pdb=" O ASN E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 271 removed outlier: 4.330A pdb=" N LEU E 251 " --> pdb=" O ASN E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 295 Processing helix chain 'E' and resid 295 through 303 Processing helix chain 'E' and resid 305 through 314 removed outlier: 3.672A pdb=" N PHE E 312 " --> pdb=" O VAL E 308 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN E 314 " --> pdb=" O ASN E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 326 removed outlier: 3.525A pdb=" N LEU E 326 " --> pdb=" O LEU E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 336 removed outlier: 3.542A pdb=" N LEU E 334 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 345 Processing helix chain 'E' and resid 348 through 379 removed outlier: 3.922A pdb=" N LEU E 352 " --> pdb=" O GLY E 348 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE E 379 " --> pdb=" O ASP E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 400 removed outlier: 3.621A pdb=" N GLN E 394 " --> pdb=" O SER E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 436 removed outlier: 3.920A pdb=" N TYR E 423 " --> pdb=" O LYS E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 499 removed outlier: 3.525A pdb=" N LEU E 462 " --> pdb=" O MET E 458 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN E 481 " --> pdb=" O GLN E 477 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR E 482 " --> pdb=" O MET E 478 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR E 485 " --> pdb=" O ASN E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 521 Processing helix chain 'E' and resid 524 through 532 Processing helix chain 'E' and resid 533 through 545 Processing helix chain 'E' and resid 545 through 552 removed outlier: 3.845A pdb=" N GLU E 551 " --> pdb=" O LYS E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 570 removed outlier: 3.649A pdb=" N GLU E 569 " --> pdb=" O ALA E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 625 removed outlier: 3.682A pdb=" N GLU E 624 " --> pdb=" O VAL E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 657 Processing helix chain 'E' and resid 657 through 668 removed outlier: 3.923A pdb=" N HIS E 662 " --> pdb=" O THR E 658 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 694 removed outlier: 3.791A pdb=" N MET E 694 " --> pdb=" O GLU E 690 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 722 removed outlier: 4.235A pdb=" N VAL E 710 " --> pdb=" O PRO E 706 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG E 712 " --> pdb=" O HIS E 708 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU E 713 " --> pdb=" O PRO E 709 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 722 " --> pdb=" O ARG E 718 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 20 removed outlier: 3.514A pdb=" N PHE F 16 " --> pdb=" O PHE F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 Processing helix chain 'F' and resid 44 through 56 removed outlier: 3.526A pdb=" N LEU F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 removed outlier: 3.745A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 147 removed outlier: 3.873A pdb=" N MET F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET F 145 " --> pdb=" O PHE F 141 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA F 147 " --> pdb=" O GLN F 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 26 removed outlier: 4.477A pdb=" N ASN G 26 " --> pdb=" O VAL G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 54 Processing helix chain 'G' and resid 56 through 61 removed outlier: 3.507A pdb=" N VAL G 60 " --> pdb=" O HIS G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 90 Processing helix chain 'G' and resid 146 through 158 Processing helix chain 'G' and resid 159 through 164 removed outlier: 3.861A pdb=" N VAL G 164 " --> pdb=" O SER G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 194 removed outlier: 3.909A pdb=" N VAL G 178 " --> pdb=" O LYS G 174 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS G 180 " --> pdb=" O GLU G 176 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS G 181 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL G 187 " --> pdb=" O ARG G 183 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER G 192 " --> pdb=" O LEU G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 242 Proline residue: G 236 - end of helix removed outlier: 3.548A pdb=" N LYS G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 271 removed outlier: 4.330A pdb=" N LEU G 251 " --> pdb=" O ASN G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 295 Processing helix chain 'G' and resid 295 through 303 Processing helix chain 'G' and resid 305 through 314 removed outlier: 3.672A pdb=" N PHE G 312 " --> pdb=" O VAL G 308 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU G 313 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN G 314 " --> pdb=" O ASN G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 326 removed outlier: 3.525A pdb=" N LEU G 326 " --> pdb=" O LEU G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 336 removed outlier: 3.542A pdb=" N LEU G 334 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 345 Processing helix chain 'G' and resid 348 through 379 removed outlier: 3.922A pdb=" N LEU G 352 " --> pdb=" O GLY G 348 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 353 " --> pdb=" O ALA G 349 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE G 379 " --> pdb=" O ASP G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 400 removed outlier: 3.621A pdb=" N GLN G 394 " --> pdb=" O SER G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 436 removed outlier: 3.920A pdb=" N TYR G 423 " --> pdb=" O LYS G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 499 removed outlier: 3.525A pdb=" N LEU G 462 " --> pdb=" O MET G 458 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN G 481 " --> pdb=" O GLN G 477 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR G 482 " --> pdb=" O MET G 478 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR G 485 " --> pdb=" O ASN G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 521 Processing helix chain 'G' and resid 524 through 532 Processing helix chain 'G' and resid 533 through 545 Processing helix chain 'G' and resid 545 through 552 removed outlier: 3.845A pdb=" N GLU G 551 " --> pdb=" O LYS G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 570 removed outlier: 3.649A pdb=" N GLU G 569 " --> pdb=" O ALA G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 620 through 625 removed outlier: 3.682A pdb=" N GLU G 624 " --> pdb=" O VAL G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 647 through 657 Processing helix chain 'G' and resid 657 through 668 removed outlier: 3.923A pdb=" N HIS G 662 " --> pdb=" O THR G 658 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER G 663 " --> pdb=" O ALA G 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 682 through 694 removed outlier: 3.791A pdb=" N MET G 694 " --> pdb=" O GLU G 690 " (cutoff:3.500A) Processing helix chain 'G' and resid 706 through 722 removed outlier: 4.235A pdb=" N VAL G 710 " --> pdb=" O PRO G 706 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG G 712 " --> pdb=" O HIS G 708 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU G 713 " --> pdb=" O PRO G 709 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU G 722 " --> pdb=" O ARG G 718 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 20 removed outlier: 3.514A pdb=" N PHE H 16 " --> pdb=" O PHE H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 40 Processing helix chain 'H' and resid 44 through 56 removed outlier: 3.526A pdb=" N LEU H 48 " --> pdb=" O THR H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 77 removed outlier: 3.745A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 147 removed outlier: 3.873A pdb=" N MET H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA H 147 " --> pdb=" O GLN H 143 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.538A pdb=" N ILE A 42 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN A 34 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN A 29 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 31 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS A 128 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 33 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 125 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 93 " --> pdb=" O ILE A 113 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 573 through 575 removed outlier: 6.921A pdb=" N ASP A 641 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 591 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP A 615 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 618 " --> pdb=" O TYR A 672 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 587 through 588 removed outlier: 4.684A pdb=" N ALA A 628 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 607 through 611 removed outlier: 6.717A pdb=" N VAL A 601 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 610 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU A 599 " --> pdb=" O ILE A 610 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.538A pdb=" N ILE C 42 " --> pdb=" O ASN C 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN C 34 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN C 29 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 31 " --> pdb=" O CYS C 128 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS C 128 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 33 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 125 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN C 93 " --> pdb=" O ILE C 113 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 573 through 575 removed outlier: 6.921A pdb=" N ASP C 641 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 591 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 615 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 618 " --> pdb=" O TYR C 672 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'C' and resid 587 through 588 removed outlier: 4.684A pdb=" N ALA C 628 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 607 through 611 removed outlier: 6.717A pdb=" N VAL C 601 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE C 610 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C 599 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.538A pdb=" N ILE E 42 " --> pdb=" O ASN E 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN E 34 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN E 29 " --> pdb=" O PHE E 130 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 31 " --> pdb=" O CYS E 128 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS E 128 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY E 33 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 125 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN E 93 " --> pdb=" O ILE E 113 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'E' and resid 573 through 575 removed outlier: 6.921A pdb=" N ASP E 641 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 591 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP E 615 " --> pdb=" O VAL E 594 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY E 618 " --> pdb=" O TYR E 672 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'E' and resid 587 through 588 removed outlier: 4.684A pdb=" N ALA E 628 " --> pdb=" O VAL E 588 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'E' and resid 607 through 611 removed outlier: 6.717A pdb=" N VAL E 601 " --> pdb=" O VAL E 608 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE E 610 " --> pdb=" O LEU E 599 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU E 599 " --> pdb=" O ILE E 610 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'G' and resid 42 through 45 removed outlier: 6.538A pdb=" N ILE G 42 " --> pdb=" O ASN G 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN G 34 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN G 29 " --> pdb=" O PHE G 130 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL G 31 " --> pdb=" O CYS G 128 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS G 128 " --> pdb=" O VAL G 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY G 33 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU G 125 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN G 93 " --> pdb=" O ILE G 113 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'G' and resid 573 through 575 removed outlier: 6.921A pdb=" N ASP G 641 " --> pdb=" O VAL G 595 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU G 591 " --> pdb=" O ILE G 645 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP G 615 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY G 618 " --> pdb=" O TYR G 672 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'G' and resid 587 through 588 removed outlier: 4.684A pdb=" N ALA G 628 " --> pdb=" O VAL G 588 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'G' and resid 607 through 611 removed outlier: 6.717A pdb=" N VAL G 601 " --> pdb=" O VAL G 608 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE G 610 " --> pdb=" O LEU G 599 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU G 599 " --> pdb=" O ILE G 610 " (cutoff:3.500A) 1504 hydrogen bonds defined for protein. 4380 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: 5.90 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5120 1.33 - 1.45: 5924 1.45 - 1.57: 14020 1.57 - 1.69: 8 1.69 - 1.81: 196 Bond restraints: 25268 Sorted by residual: bond pdb=" CA PRO C 705 " pdb=" C PRO C 705 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.54e+00 bond pdb=" CA PRO E 705 " pdb=" C PRO E 705 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.54e+00 bond pdb=" CA PRO A 705 " pdb=" C PRO A 705 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.54e+00 bond pdb=" CA PRO G 705 " pdb=" C PRO G 705 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.54e+00 bond pdb=" CA GLU A 313 " pdb=" C GLU A 313 " ideal model delta sigma weight residual 1.522 1.560 -0.038 1.39e-02 5.18e+03 7.48e+00 ... (remaining 25263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 26480 1.56 - 3.12: 7244 3.12 - 4.68: 700 4.68 - 6.24: 140 6.24 - 7.80: 20 Bond angle restraints: 34584 Sorted by residual: angle pdb=" O VAL G 235 " pdb=" C VAL G 235 " pdb=" N PRO G 236 " ideal model delta sigma weight residual 120.07 124.14 -4.07 7.10e-01 1.98e+00 3.28e+01 angle pdb=" O VAL A 235 " pdb=" C VAL A 235 " pdb=" N PRO A 236 " ideal model delta sigma weight residual 120.07 124.14 -4.07 7.10e-01 1.98e+00 3.28e+01 angle pdb=" O VAL E 235 " pdb=" C VAL E 235 " pdb=" N PRO E 236 " ideal model delta sigma weight residual 120.07 124.14 -4.07 7.10e-01 1.98e+00 3.28e+01 angle pdb=" O VAL C 235 " pdb=" C VAL C 235 " pdb=" N PRO C 236 " ideal model delta sigma weight residual 120.07 124.14 -4.07 7.10e-01 1.98e+00 3.28e+01 angle pdb=" CA VAL E 235 " pdb=" C VAL E 235 " pdb=" N PRO E 236 " ideal model delta sigma weight residual 121.00 116.49 4.51 8.30e-01 1.45e+00 2.95e+01 ... (remaining 34579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.29: 12808 13.29 - 26.58: 1192 26.58 - 39.87: 472 39.87 - 53.16: 108 53.16 - 66.45: 24 Dihedral angle restraints: 14604 sinusoidal: 4728 harmonic: 9876 Sorted by residual: dihedral pdb=" CA ILE C 233 " pdb=" C ILE C 233 " pdb=" N LEU C 234 " pdb=" CA LEU C 234 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ILE G 233 " pdb=" C ILE G 233 " pdb=" N LEU G 234 " pdb=" CA LEU G 234 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ILE E 233 " pdb=" C ILE E 233 " pdb=" N LEU E 234 " pdb=" CA LEU E 234 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 14601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3376 0.092 - 0.184: 648 0.184 - 0.276: 44 0.276 - 0.369: 20 0.369 - 0.461: 12 Chirality restraints: 4100 Sorted by residual: chirality pdb=" C4 NAG C 901 " pdb=" C3 NAG C 901 " pdb=" C5 NAG C 901 " pdb=" O4 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.53 -2.07 -0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" C4 NAG E 901 " pdb=" C3 NAG E 901 " pdb=" C5 NAG E 901 " pdb=" O4 NAG E 901 " both_signs ideal model delta sigma weight residual False -2.53 -2.07 -0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" C4 NAG G 901 " pdb=" C3 NAG G 901 " pdb=" C5 NAG G 901 " pdb=" O4 NAG G 901 " both_signs ideal model delta sigma weight residual False -2.53 -2.07 -0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 4097 not shown) Planarity restraints: 4408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 65 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO D 66 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 66 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 66 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 65 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO B 66 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 66 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 66 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 65 " 0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO F 66 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO F 66 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 66 " 0.030 5.00e-02 4.00e+02 ... (remaining 4405 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 7912 2.85 - 3.36: 25012 3.36 - 3.87: 39992 3.87 - 4.39: 42628 4.39 - 4.90: 71054 Nonbonded interactions: 186598 Sorted by model distance: nonbonded pdb=" O PHE C 429 " pdb=" OG1 THR C 432 " model vdw 2.336 3.040 nonbonded pdb=" O PHE G 429 " pdb=" OG1 THR G 432 " model vdw 2.336 3.040 nonbonded pdb=" O PHE E 429 " pdb=" OG1 THR E 432 " model vdw 2.336 3.040 nonbonded pdb=" O PHE A 429 " pdb=" OG1 THR A 432 " model vdw 2.336 3.040 nonbonded pdb=" O LEU E 463 " pdb=" OG1 THR E 466 " model vdw 2.393 3.040 ... (remaining 186593 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 1.600 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: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 26.290 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 0.008 0.038 25272 Z= 0.540 Angle : 1.363 7.802 34596 Z= 1.031 Chirality : 0.074 0.461 4100 Planarity : 0.005 0.054 4404 Dihedral : 13.266 66.453 8204 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.31 % Favored : 92.57 % Rotamer: Outliers : 0.35 % Allowed : 7.03 % Favored : 92.62 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 3340 helix: 1.54 (0.10), residues: 1908 sheet: -3.18 (0.35), residues: 148 loop : -2.46 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 647 TYR 0.028 0.002 TYR E 237 PHE 0.026 0.002 PHE A 323 TRP 0.024 0.002 TRP A 370 HIS 0.005 0.001 HIS G 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.54 (25268) covalent geometry : angle 1.36264 / 1.03 (34584) hydrogen bonds : bond 0.16584 / 11.45 ( 1504) hydrogen bonds : angle 5.51885 / 4.10 ( 4380) link_NAG-ASN : bond 0.00214 / 0.11 ( 4) link_NAG-ASN : angle 2.74950 / 1.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.954 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: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9819 (mtm) cc_final: 0.9557 (mtm) REVERT: A 431 MET cc_start: 0.9904 (tpt) cc_final: 0.9256 (mmm) REVERT: A 478 MET cc_start: 0.9665 (ptp) cc_final: 0.9314 (ppp) REVERT: A 488 MET cc_start: 0.9763 (ttp) cc_final: 0.9439 (tmm) REVERT: B 99 TYR cc_start: 0.9708 (m-80) cc_final: 0.9269 (m-80) REVERT: B 145 MET cc_start: 0.9163 (mmm) cc_final: 0.8788 (mtp) REVERT: C 99 MET cc_start: 0.9819 (mtm) cc_final: 0.9557 (mtm) REVERT: C 431 MET cc_start: 0.9904 (tpt) cc_final: 0.9261 (mmm) REVERT: C 478 MET cc_start: 0.9665 (ptp) cc_final: 0.9314 (ppp) REVERT: C 488 MET cc_start: 0.9763 (ttp) cc_final: 0.9439 (tmm) REVERT: D 99 TYR cc_start: 0.9707 (m-80) cc_final: 0.9269 (m-80) REVERT: D 145 MET cc_start: 0.9164 (mmm) cc_final: 0.8789 (mtp) REVERT: E 99 MET cc_start: 0.9819 (mtm) cc_final: 0.9555 (mtm) REVERT: E 431 MET cc_start: 0.9904 (tpt) cc_final: 0.9261 (mmm) REVERT: E 478 MET cc_start: 0.9665 (ptp) cc_final: 0.9314 (ppp) REVERT: E 488 MET cc_start: 0.9763 (ttp) cc_final: 0.9439 (tmm) REVERT: F 99 TYR cc_start: 0.9707 (m-80) cc_final: 0.9269 (m-80) REVERT: F 145 MET cc_start: 0.9163 (mmm) cc_final: 0.8789 (mtp) REVERT: G 99 MET cc_start: 0.9819 (mtm) cc_final: 0.9556 (mtm) REVERT: G 431 MET cc_start: 0.9904 (tpt) cc_final: 0.9262 (mmm) REVERT: G 478 MET cc_start: 0.9665 (ptp) cc_final: 0.9314 (ppp) REVERT: G 488 MET cc_start: 0.9763 (ttp) cc_final: 0.9439 (tmm) REVERT: H 99 TYR cc_start: 0.9708 (m-80) cc_final: 0.9269 (m-80) REVERT: H 145 MET cc_start: 0.9163 (mmm) cc_final: 0.8788 (mtp) outliers start: 8 outliers final: 0 residues processed: 172 average time/residue: 0.1596 time to fit residues: 45.4805 Evaluate side-chains 128 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN A 667 ASN C 441 ASN C 667 ASN E 441 ASN E 667 ASN G 441 ASN G 667 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.033431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.028716 restraints weight = 378257.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.029202 restraints weight = 225566.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.029527 restraints weight = 157555.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.029700 restraints weight = 121518.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.029915 restraints weight = 103588.289| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 25272 Z= 0.234 Angle : 0.622 7.240 34596 Z= 0.336 Chirality : 0.040 0.138 4100 Planarity : 0.004 0.048 4404 Dihedral : 4.696 20.181 3596 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.41 % Allowed : 10.28 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.15), residues: 3340 helix: 2.47 (0.12), residues: 2000 sheet: -2.66 (0.28), residues: 216 loop : -1.70 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 387 TYR 0.016 0.002 TYR G 44 PHE 0.019 0.002 PHE A 241 TRP 0.021 0.002 TRP E 370 HIS 0.005 0.001 HIS C 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.23 (25268) covalent geometry : angle 0.62015 / 0.34 (34584) hydrogen bonds : bond 0.03947 / 2.72 ( 1504) hydrogen bonds : angle 4.18728 / 3.11 ( 4380) link_NAG-ASN : bond 0.01144 / 0.57 ( 4) link_NAG-ASN : angle 2.28422 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.9584 (ttp) cc_final: 0.9264 (mmp) REVERT: A 568 MET cc_start: 0.9361 (mmm) cc_final: 0.8931 (mmm) REVERT: B 145 MET cc_start: 0.8495 (mmm) cc_final: 0.8231 (mtp) REVERT: C 431 MET cc_start: 0.9688 (tpt) cc_final: 0.9133 (tpp) REVERT: C 519 MET cc_start: 0.9566 (ttp) cc_final: 0.9257 (mmp) REVERT: C 568 MET cc_start: 0.9366 (mmm) cc_final: 0.8936 (mmm) REVERT: D 145 MET cc_start: 0.8471 (mmm) cc_final: 0.8219 (mtp) REVERT: E 431 MET cc_start: 0.9687 (tpt) cc_final: 0.9132 (tpp) REVERT: E 519 MET cc_start: 0.9560 (ttp) cc_final: 0.9256 (mmp) REVERT: E 568 MET cc_start: 0.9366 (mmm) cc_final: 0.8937 (mmm) REVERT: F 145 MET cc_start: 0.8453 (mmm) cc_final: 0.8212 (mtp) REVERT: G 431 MET cc_start: 0.9692 (tpt) cc_final: 0.9145 (tpp) REVERT: G 519 MET cc_start: 0.9578 (ttp) cc_final: 0.9262 (mmp) REVERT: G 568 MET cc_start: 0.9362 (mmm) cc_final: 0.8933 (mmm) REVERT: H 145 MET cc_start: 0.8470 (mmm) cc_final: 0.8220 (mtp) outliers start: 32 outliers final: 4 residues processed: 144 average time/residue: 0.1437 time to fit residues: 35.8223 Evaluate side-chains 122 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain G residue 352 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 321 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 265 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 280 optimal weight: 8.9990 chunk 14 optimal weight: 30.0000 chunk 297 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.031553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.028715 restraints weight = 288899.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.029161 restraints weight = 188499.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.029506 restraints weight = 134560.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.029674 restraints weight = 108050.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.029703 restraints weight = 96386.490| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25272 Z= 0.168 Angle : 0.544 8.191 34596 Z= 0.287 Chirality : 0.038 0.170 4100 Planarity : 0.004 0.053 4404 Dihedral : 4.281 17.368 3596 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.10 % Allowed : 12.39 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.16), residues: 3340 helix: 2.59 (0.12), residues: 2004 sheet: -2.48 (0.26), residues: 232 loop : -1.35 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 387 TYR 0.012 0.002 TYR E 44 PHE 0.016 0.001 PHE A 359 TRP 0.016 0.002 TRP G 370 HIS 0.003 0.001 HIS G 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (25268) covalent geometry : angle 0.54347 / 0.29 (34584) hydrogen bonds : bond 0.03347 / 2.30 ( 1504) hydrogen bonds : angle 3.92348 / 2.91 ( 4380) link_NAG-ASN : bond 0.00543 / 0.27 ( 4) link_NAG-ASN : angle 1.35418 / 0.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.111 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 431 MET cc_start: 0.9475 (tpp) cc_final: 0.9258 (tpp) REVERT: A 435 THR cc_start: 0.9407 (OUTLIER) cc_final: 0.9052 (p) REVERT: A 457 MET cc_start: 0.9440 (ptm) cc_final: 0.9237 (ptm) REVERT: A 488 MET cc_start: 0.9265 (tmm) cc_final: 0.9044 (ppp) REVERT: A 519 MET cc_start: 0.9775 (ttp) cc_final: 0.9318 (mmp) REVERT: A 568 MET cc_start: 0.9459 (mmm) cc_final: 0.9133 (mmm) REVERT: C 431 MET cc_start: 0.9649 (tpt) cc_final: 0.9406 (tpp) REVERT: C 457 MET cc_start: 0.9445 (ptm) cc_final: 0.9243 (ptm) REVERT: C 488 MET cc_start: 0.9265 (tmm) cc_final: 0.9047 (ppp) REVERT: C 519 MET cc_start: 0.9768 (ttp) cc_final: 0.9312 (mmp) REVERT: C 568 MET cc_start: 0.9462 (mmm) cc_final: 0.9136 (mmm) REVERT: E 431 MET cc_start: 0.9650 (tpt) cc_final: 0.9404 (tpp) REVERT: E 457 MET cc_start: 0.9435 (ptm) cc_final: 0.9233 (ptm) REVERT: E 488 MET cc_start: 0.9265 (tmm) cc_final: 0.9046 (ppp) REVERT: E 519 MET cc_start: 0.9771 (ttp) cc_final: 0.9312 (mmp) REVERT: E 568 MET cc_start: 0.9458 (mmm) cc_final: 0.9134 (mmm) REVERT: G 431 MET cc_start: 0.9635 (tpt) cc_final: 0.9403 (tpp) REVERT: G 457 MET cc_start: 0.9406 (ptm) cc_final: 0.9121 (ptm) REVERT: G 478 MET cc_start: 0.9363 (ptm) cc_final: 0.9135 (ptm) REVERT: G 488 MET cc_start: 0.9266 (tmm) cc_final: 0.9045 (ppp) REVERT: G 519 MET cc_start: 0.9775 (ttp) cc_final: 0.9317 (mmp) REVERT: G 568 MET cc_start: 0.9460 (mmm) cc_final: 0.9131 (mmm) outliers start: 25 outliers final: 4 residues processed: 151 average time/residue: 0.1356 time to fit residues: 36.5936 Evaluate side-chains 126 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain G residue 620 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 13 optimal weight: 0.0030 chunk 124 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 chunk 281 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 19 optimal weight: 30.0000 chunk 194 optimal weight: 0.0870 overall best weight: 2.0172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.031882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.028884 restraints weight = 283443.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.029371 restraints weight = 186252.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.029726 restraints weight = 128908.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.029899 restraints weight = 102952.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.029942 restraints weight = 91908.254| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25272 Z= 0.108 Angle : 0.523 10.557 34596 Z= 0.264 Chirality : 0.038 0.187 4100 Planarity : 0.003 0.054 4404 Dihedral : 4.062 16.238 3596 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.27 % Allowed : 11.73 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.16), residues: 3340 helix: 2.73 (0.12), residues: 1968 sheet: -2.30 (0.27), residues: 232 loop : -1.05 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 387 TYR 0.011 0.001 TYR A 464 PHE 0.013 0.001 PHE E 617 TRP 0.014 0.001 TRP G 370 HIS 0.001 0.000 HIS A 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (25268) covalent geometry : angle 0.52224 / 0.26 (34584) hydrogen bonds : bond 0.02942 / 2.03 ( 1504) hydrogen bonds : angle 3.69321 / 2.74 ( 4380) link_NAG-ASN : bond 0.00273 / 0.14 ( 4) link_NAG-ASN : angle 1.29241 / 0.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.965 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 269 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8539 (m-80) REVERT: A 431 MET cc_start: 0.9566 (tpp) cc_final: 0.9311 (tpp) REVERT: A 435 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.8954 (p) REVERT: A 519 MET cc_start: 0.9772 (ttp) cc_final: 0.9299 (mmp) REVERT: A 560 ASP cc_start: 0.9385 (OUTLIER) cc_final: 0.8761 (t0) REVERT: C 269 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8554 (m-80) REVERT: C 431 MET cc_start: 0.9726 (tpt) cc_final: 0.9456 (tpp) REVERT: C 519 MET cc_start: 0.9768 (ttp) cc_final: 0.9295 (mmp) REVERT: C 560 ASP cc_start: 0.9384 (OUTLIER) cc_final: 0.8760 (t0) REVERT: E 269 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8547 (m-80) REVERT: E 431 MET cc_start: 0.9722 (tpt) cc_final: 0.9450 (tpp) REVERT: E 519 MET cc_start: 0.9771 (ttp) cc_final: 0.9296 (mmp) REVERT: E 560 ASP cc_start: 0.9386 (OUTLIER) cc_final: 0.8762 (t0) REVERT: G 269 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8549 (m-80) REVERT: G 431 MET cc_start: 0.9692 (tpt) cc_final: 0.9445 (tpp) REVERT: G 457 MET cc_start: 0.9193 (ptm) cc_final: 0.8958 (ptm) REVERT: G 519 MET cc_start: 0.9772 (ttp) cc_final: 0.9298 (mmp) REVERT: G 560 ASP cc_start: 0.9388 (OUTLIER) cc_final: 0.8768 (t0) outliers start: 29 outliers final: 8 residues processed: 145 average time/residue: 0.1271 time to fit residues: 32.6948 Evaluate side-chains 140 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain E residue 269 PHE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 560 ASP Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain G residue 478 MET Chi-restraints excluded: chain G residue 560 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 312 optimal weight: 20.0000 chunk 333 optimal weight: 8.9990 chunk 190 optimal weight: 0.3980 chunk 267 optimal weight: 0.5980 chunk 309 optimal weight: 9.9990 chunk 189 optimal weight: 0.5980 chunk 72 optimal weight: 50.0000 chunk 325 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 314 optimal weight: 20.0000 chunk 211 optimal weight: 5.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.031843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.028839 restraints weight = 280844.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.029069 restraints weight = 174338.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.029324 restraints weight = 149143.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.029545 restraints weight = 129534.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.029663 restraints weight = 113721.747| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25272 Z= 0.114 Angle : 0.535 10.244 34596 Z= 0.265 Chirality : 0.038 0.206 4100 Planarity : 0.003 0.055 4404 Dihedral : 3.914 15.558 3596 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.41 % Allowed : 11.91 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.15), residues: 3340 helix: 2.71 (0.12), residues: 1972 sheet: -2.17 (0.27), residues: 232 loop : -0.94 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 387 TYR 0.010 0.001 TYR C 464 PHE 0.023 0.001 PHE B 141 TRP 0.013 0.001 TRP G 370 HIS 0.002 0.001 HIS C 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (25268) covalent geometry : angle 0.53487 / 0.26 (34584) hydrogen bonds : bond 0.02789 / 1.92 ( 1504) hydrogen bonds : angle 3.64597 / 2.70 ( 4380) link_NAG-ASN : bond 0.00368 / 0.18 ( 4) link_NAG-ASN : angle 1.29947 / 0.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8694 (m-80) REVERT: A 431 MET cc_start: 0.9547 (tpp) cc_final: 0.9315 (tpp) REVERT: A 435 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.8844 (p) REVERT: A 519 MET cc_start: 0.9806 (ttp) cc_final: 0.9328 (mmp) REVERT: A 560 ASP cc_start: 0.9390 (OUTLIER) cc_final: 0.8814 (t0) REVERT: B 145 MET cc_start: 0.8497 (mtp) cc_final: 0.8199 (ptp) REVERT: C 269 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8703 (m-80) REVERT: C 431 MET cc_start: 0.9681 (tpt) cc_final: 0.9315 (tpp) REVERT: C 435 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8657 (p) REVERT: C 519 MET cc_start: 0.9802 (ttp) cc_final: 0.9321 (mmp) REVERT: C 560 ASP cc_start: 0.9391 (OUTLIER) cc_final: 0.8813 (t0) REVERT: D 145 MET cc_start: 0.8499 (mtp) cc_final: 0.8202 (ptp) REVERT: E 269 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8708 (m-80) REVERT: E 431 MET cc_start: 0.9683 (tpt) cc_final: 0.9199 (mmm) REVERT: E 519 MET cc_start: 0.9803 (ttp) cc_final: 0.9322 (mmp) REVERT: E 560 ASP cc_start: 0.9392 (OUTLIER) cc_final: 0.8817 (t0) REVERT: F 145 MET cc_start: 0.8486 (mtp) cc_final: 0.8191 (ptp) REVERT: G 269 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8705 (m-80) REVERT: G 431 MET cc_start: 0.9650 (tpt) cc_final: 0.9308 (tpp) REVERT: G 435 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.8763 (p) REVERT: G 519 MET cc_start: 0.9804 (ttp) cc_final: 0.9324 (mmp) REVERT: G 560 ASP cc_start: 0.9392 (OUTLIER) cc_final: 0.8822 (t0) REVERT: H 145 MET cc_start: 0.8488 (mtp) cc_final: 0.8192 (ptp) outliers start: 32 outliers final: 13 residues processed: 147 average time/residue: 0.1364 time to fit residues: 35.6312 Evaluate side-chains 144 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain E residue 269 PHE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 560 ASP Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain G residue 435 THR Chi-restraints excluded: chain G residue 478 MET Chi-restraints excluded: chain G residue 560 ASP Chi-restraints excluded: chain G residue 620 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 321 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 chunk 303 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 252 optimal weight: 6.9990 chunk 287 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 316 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 ASN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS C 93 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 HIS E 93 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 HIS G 93 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.030984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.028016 restraints weight = 297423.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.028433 restraints weight = 188714.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.028812 restraints weight = 144172.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.029010 restraints weight = 115170.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.029052 restraints weight = 102450.962| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 25272 Z= 0.203 Angle : 0.585 10.205 34596 Z= 0.297 Chirality : 0.039 0.248 4100 Planarity : 0.004 0.055 4404 Dihedral : 4.130 16.212 3596 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.63 % Allowed : 11.78 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.16), residues: 3340 helix: 2.69 (0.12), residues: 1968 sheet: -2.38 (0.27), residues: 240 loop : -0.82 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 387 TYR 0.017 0.002 TYR G 71 PHE 0.022 0.002 PHE G 69 TRP 0.012 0.002 TRP C 108 HIS 0.004 0.001 HIS C 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 (25268) covalent geometry : angle 0.58436 / 0.30 (34584) hydrogen bonds : bond 0.03028 / 2.08 ( 1504) hydrogen bonds : angle 3.81527 / 2.83 ( 4380) link_NAG-ASN : bond 0.00792 / 0.40 ( 4) link_NAG-ASN : angle 1.51133 / 0.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8737 (m-80) REVERT: A 431 MET cc_start: 0.9610 (tpp) cc_final: 0.9249 (mmm) REVERT: A 435 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8772 (t) REVERT: A 519 MET cc_start: 0.9816 (ttp) cc_final: 0.9379 (mmp) REVERT: A 560 ASP cc_start: 0.9428 (OUTLIER) cc_final: 0.8881 (t0) REVERT: A 568 MET cc_start: 0.9298 (mmm) cc_final: 0.8790 (mmm) REVERT: B 145 MET cc_start: 0.8640 (mtp) cc_final: 0.8381 (ptp) REVERT: C 269 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8734 (m-80) REVERT: C 431 MET cc_start: 0.9701 (tpt) cc_final: 0.9286 (mmm) REVERT: C 435 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.8726 (t) REVERT: C 519 MET cc_start: 0.9814 (ttp) cc_final: 0.9375 (mmp) REVERT: C 560 ASP cc_start: 0.9428 (OUTLIER) cc_final: 0.8880 (t0) REVERT: C 568 MET cc_start: 0.9300 (mmm) cc_final: 0.8795 (mmm) REVERT: D 145 MET cc_start: 0.8640 (mtp) cc_final: 0.8382 (ptp) REVERT: E 269 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8749 (m-80) REVERT: E 431 MET cc_start: 0.9707 (tpt) cc_final: 0.9286 (mmm) REVERT: E 435 THR cc_start: 0.9346 (OUTLIER) cc_final: 0.8789 (t) REVERT: E 519 MET cc_start: 0.9813 (ttp) cc_final: 0.9372 (mmp) REVERT: E 560 ASP cc_start: 0.9428 (OUTLIER) cc_final: 0.8883 (t0) REVERT: E 568 MET cc_start: 0.9303 (mmm) cc_final: 0.8798 (mmm) REVERT: F 145 MET cc_start: 0.8628 (mtp) cc_final: 0.8371 (ptp) REVERT: G 269 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8734 (m-80) REVERT: G 431 MET cc_start: 0.9685 (OUTLIER) cc_final: 0.9221 (mmm) REVERT: G 519 MET cc_start: 0.9816 (ttp) cc_final: 0.9378 (mmp) REVERT: G 560 ASP cc_start: 0.9428 (OUTLIER) cc_final: 0.8889 (t0) REVERT: G 568 MET cc_start: 0.9294 (mmm) cc_final: 0.8795 (mmm) REVERT: H 145 MET cc_start: 0.8628 (mtp) cc_final: 0.8371 (ptp) outliers start: 37 outliers final: 17 residues processed: 147 average time/residue: 0.1440 time to fit residues: 36.9649 Evaluate side-chains 148 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 269 PHE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 560 ASP Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain G residue 431 MET Chi-restraints excluded: chain G residue 435 THR Chi-restraints excluded: chain G residue 478 MET Chi-restraints excluded: chain G residue 560 ASP Chi-restraints excluded: chain G residue 620 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 201 optimal weight: 8.9990 chunk 254 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 311 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 331 optimal weight: 8.9990 chunk 273 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 HIS C 85 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 HIS E 85 GLN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 HIS G 85 GLN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 708 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.030256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.027352 restraints weight = 322047.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.027761 restraints weight = 196842.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.028141 restraints weight = 145266.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.028315 restraints weight = 114715.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.028522 restraints weight = 102354.981| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25272 Z= 0.246 Angle : 0.625 11.607 34596 Z= 0.319 Chirality : 0.039 0.166 4100 Planarity : 0.004 0.055 4404 Dihedral : 4.264 16.614 3596 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.23 % Allowed : 12.74 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.15), residues: 3340 helix: 2.46 (0.12), residues: 1944 sheet: -2.00 (0.28), residues: 204 loop : -0.88 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 387 TYR 0.016 0.002 TYR E 71 PHE 0.038 0.002 PHE A 69 TRP 0.013 0.002 TRP G 370 HIS 0.004 0.001 HIS A 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.25 (25268) covalent geometry : angle 0.62432 / 0.32 (34584) hydrogen bonds : bond 0.03316 / 2.28 ( 1504) hydrogen bonds : angle 3.97644 / 2.95 ( 4380) link_NAG-ASN : bond 0.00817 / 0.41 ( 4) link_NAG-ASN : angle 1.44864 / 0.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8819 (mmm) cc_final: 0.8398 (mmm) REVERT: A 431 MET cc_start: 0.9797 (tpp) cc_final: 0.9198 (mmm) REVERT: A 435 THR cc_start: 0.9581 (OUTLIER) cc_final: 0.8890 (p) REVERT: A 519 MET cc_start: 0.9651 (ttp) cc_final: 0.9346 (mmp) REVERT: B 145 MET cc_start: 0.8250 (mtp) cc_final: 0.7993 (ptp) REVERT: C 61 MET cc_start: 0.8878 (mmm) cc_final: 0.8416 (mmm) REVERT: C 431 MET cc_start: 0.9856 (tpt) cc_final: 0.9192 (mmm) REVERT: C 519 MET cc_start: 0.9629 (ttp) cc_final: 0.9338 (mmp) REVERT: D 145 MET cc_start: 0.8233 (mtp) cc_final: 0.7978 (ptp) REVERT: E 61 MET cc_start: 0.8858 (mmm) cc_final: 0.8411 (mmm) REVERT: E 431 MET cc_start: 0.9855 (tpt) cc_final: 0.9177 (mmm) REVERT: E 519 MET cc_start: 0.9632 (ttp) cc_final: 0.9339 (mmp) REVERT: F 145 MET cc_start: 0.8224 (mtp) cc_final: 0.7973 (ptp) REVERT: G 61 MET cc_start: 0.8818 (mmm) cc_final: 0.8395 (mmm) REVERT: G 431 MET cc_start: 0.9847 (tpt) cc_final: 0.9177 (mmm) REVERT: G 478 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.9179 (ptm) REVERT: G 519 MET cc_start: 0.9665 (ttp) cc_final: 0.9352 (mmp) REVERT: H 145 MET cc_start: 0.8247 (mtp) cc_final: 0.7991 (ptp) outliers start: 28 outliers final: 18 residues processed: 135 average time/residue: 0.1475 time to fit residues: 34.6052 Evaluate side-chains 137 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain G residue 435 THR Chi-restraints excluded: chain G residue 448 ILE Chi-restraints excluded: chain G residue 478 MET Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 222 optimal weight: 5.9990 chunk 315 optimal weight: 10.0000 chunk 246 optimal weight: 40.0000 chunk 24 optimal weight: 10.0000 chunk 317 optimal weight: 6.9990 chunk 306 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.030227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.027220 restraints weight = 310070.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.027600 restraints weight = 197476.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.027925 restraints weight = 149353.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.028179 restraints weight = 119083.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.028342 restraints weight = 102084.114| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 25272 Z= 0.204 Angle : 0.595 10.699 34596 Z= 0.299 Chirality : 0.038 0.131 4100 Planarity : 0.004 0.055 4404 Dihedral : 4.206 15.736 3596 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.67 % Allowed : 12.48 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.15), residues: 3340 helix: 2.48 (0.12), residues: 1944 sheet: -1.75 (0.31), residues: 204 loop : -0.77 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 387 TYR 0.013 0.002 TYR E 71 PHE 0.035 0.002 PHE A 69 TRP 0.013 0.002 TRP A 370 HIS 0.003 0.001 HIS E 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 (25268) covalent geometry : angle 0.59516 / 0.30 (34584) hydrogen bonds : bond 0.03111 / 2.14 ( 1504) hydrogen bonds : angle 3.92602 / 2.91 ( 4380) link_NAG-ASN : bond 0.00576 / 0.29 ( 4) link_NAG-ASN : angle 0.95944 / 0.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.9807 (tpp) cc_final: 0.9225 (mmm) REVERT: A 435 THR cc_start: 0.9552 (OUTLIER) cc_final: 0.8819 (p) REVERT: A 519 MET cc_start: 0.9609 (ttp) cc_final: 0.9327 (mmp) REVERT: A 568 MET cc_start: 0.9434 (mmm) cc_final: 0.8811 (mmm) REVERT: B 145 MET cc_start: 0.8129 (mtp) cc_final: 0.7864 (ptp) REVERT: C 431 MET cc_start: 0.9858 (OUTLIER) cc_final: 0.9320 (mmm) REVERT: C 435 THR cc_start: 0.9578 (OUTLIER) cc_final: 0.9054 (t) REVERT: C 519 MET cc_start: 0.9575 (ttp) cc_final: 0.9317 (mmp) REVERT: C 568 MET cc_start: 0.9438 (mmm) cc_final: 0.8809 (mmm) REVERT: D 145 MET cc_start: 0.8104 (mtp) cc_final: 0.7843 (ptp) REVERT: E 431 MET cc_start: 0.9855 (OUTLIER) cc_final: 0.9237 (mmm) REVERT: E 519 MET cc_start: 0.9575 (ttp) cc_final: 0.9315 (mmp) REVERT: E 568 MET cc_start: 0.9434 (mmm) cc_final: 0.8812 (mmm) REVERT: F 145 MET cc_start: 0.8103 (mtp) cc_final: 0.7844 (ptp) REVERT: G 431 MET cc_start: 0.9851 (OUTLIER) cc_final: 0.9241 (mmm) REVERT: G 478 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.9165 (ptm) REVERT: G 519 MET cc_start: 0.9611 (ttp) cc_final: 0.9328 (mmp) REVERT: G 568 MET cc_start: 0.9433 (mmm) cc_final: 0.8808 (mmm) REVERT: H 145 MET cc_start: 0.8135 (mtp) cc_final: 0.7869 (ptp) outliers start: 38 outliers final: 24 residues processed: 142 average time/residue: 0.1359 time to fit residues: 34.5289 Evaluate side-chains 149 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain G residue 431 MET Chi-restraints excluded: chain G residue 435 THR Chi-restraints excluded: chain G residue 478 MET Chi-restraints excluded: chain G residue 620 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 206 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 185 optimal weight: 7.9990 chunk 229 optimal weight: 30.0000 chunk 306 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 234 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.030567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.027618 restraints weight = 307434.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.028035 restraints weight = 194663.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.028387 restraints weight = 145031.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.028621 restraints weight = 116151.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.028703 restraints weight = 99756.462| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25272 Z= 0.140 Angle : 0.570 11.140 34596 Z= 0.279 Chirality : 0.038 0.128 4100 Planarity : 0.003 0.055 4404 Dihedral : 4.048 15.018 3596 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.45 % Allowed : 13.40 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.15), residues: 3340 helix: 2.60 (0.12), residues: 1944 sheet: -1.56 (0.32), residues: 204 loop : -0.72 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 537 TYR 0.011 0.001 TYR G 71 PHE 0.027 0.001 PHE G 69 TRP 0.014 0.001 TRP C 370 HIS 0.002 0.001 HIS A 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (25268) covalent geometry : angle 0.56958 / 0.28 (34584) hydrogen bonds : bond 0.02827 / 1.95 ( 1504) hydrogen bonds : angle 3.79164 / 2.81 ( 4380) link_NAG-ASN : bond 0.00279 / 0.14 ( 4) link_NAG-ASN : angle 0.55161 / 0.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.9829 (tpp) cc_final: 0.9605 (tpp) REVERT: A 435 THR cc_start: 0.9528 (OUTLIER) cc_final: 0.9207 (p) REVERT: A 478 MET cc_start: 0.9349 (ptm) cc_final: 0.9127 (ptm) REVERT: A 519 MET cc_start: 0.9648 (ttp) cc_final: 0.9315 (mmp) REVERT: A 568 MET cc_start: 0.9414 (mmm) cc_final: 0.8790 (mmm) REVERT: C 431 MET cc_start: 0.9871 (OUTLIER) cc_final: 0.9352 (mmm) REVERT: C 435 THR cc_start: 0.9577 (OUTLIER) cc_final: 0.9032 (t) REVERT: C 478 MET cc_start: 0.9348 (ptm) cc_final: 0.9126 (ptm) REVERT: C 519 MET cc_start: 0.9612 (ttp) cc_final: 0.9300 (mmp) REVERT: C 568 MET cc_start: 0.9421 (mmm) cc_final: 0.8801 (mmm) REVERT: D 145 MET cc_start: 0.8172 (mtp) cc_final: 0.7889 (ptp) REVERT: E 431 MET cc_start: 0.9869 (OUTLIER) cc_final: 0.9347 (mmm) REVERT: E 435 THR cc_start: 0.9581 (OUTLIER) cc_final: 0.9030 (t) REVERT: E 478 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.9120 (ptm) REVERT: E 519 MET cc_start: 0.9633 (ttp) cc_final: 0.9308 (mmp) REVERT: E 568 MET cc_start: 0.9417 (mmm) cc_final: 0.8796 (mmm) REVERT: G 431 MET cc_start: 0.9859 (OUTLIER) cc_final: 0.9353 (mmm) REVERT: G 435 THR cc_start: 0.9592 (OUTLIER) cc_final: 0.9043 (t) REVERT: G 478 MET cc_start: 0.9337 (ptm) cc_final: 0.9116 (ptm) REVERT: G 519 MET cc_start: 0.9657 (ttp) cc_final: 0.9317 (mmp) REVERT: G 568 MET cc_start: 0.9410 (mmm) cc_final: 0.8790 (mmm) outliers start: 33 outliers final: 17 residues processed: 143 average time/residue: 0.1282 time to fit residues: 33.0216 Evaluate side-chains 144 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain G residue 431 MET Chi-restraints excluded: chain G residue 435 THR Chi-restraints excluded: chain G residue 448 ILE Chi-restraints excluded: chain G residue 620 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 10 optimal weight: 8.9990 chunk 315 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 chunk 275 optimal weight: 20.0000 chunk 206 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.030067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.027092 restraints weight = 314020.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.027521 restraints weight = 198736.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.027827 restraints weight = 146398.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.028073 restraints weight = 117534.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.028264 restraints weight = 101029.273| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 25272 Z= 0.224 Angle : 0.615 10.607 34596 Z= 0.311 Chirality : 0.039 0.166 4100 Planarity : 0.004 0.055 4404 Dihedral : 4.194 16.073 3596 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.23 % Allowed : 13.71 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.15), residues: 3340 helix: 2.50 (0.12), residues: 1944 sheet: -1.33 (0.37), residues: 160 loop : -0.81 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 387 TYR 0.015 0.002 TYR A 71 PHE 0.022 0.002 PHE C 69 TRP 0.011 0.002 TRP A 370 HIS 0.004 0.001 HIS C 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.22 (25268) covalent geometry : angle 0.61466 / 0.31 (34584) hydrogen bonds : bond 0.03148 / 2.16 ( 1504) hydrogen bonds : angle 3.99678 / 2.96 ( 4380) link_NAG-ASN : bond 0.00686 / 0.34 ( 4) link_NAG-ASN : angle 0.64402 / 0.32 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.9858 (tpp) cc_final: 0.9254 (mmm) REVERT: A 435 THR cc_start: 0.9616 (OUTLIER) cc_final: 0.8871 (p) REVERT: A 478 MET cc_start: 0.9340 (ptm) cc_final: 0.9080 (ptm) REVERT: A 519 MET cc_start: 0.9620 (ttp) cc_final: 0.9345 (mmp) REVERT: B 145 MET cc_start: 0.8222 (mtp) cc_final: 0.7944 (ptp) REVERT: C 431 MET cc_start: 0.9861 (OUTLIER) cc_final: 0.9317 (mmm) REVERT: C 478 MET cc_start: 0.9340 (ptm) cc_final: 0.9081 (ptm) REVERT: C 519 MET cc_start: 0.9591 (ttp) cc_final: 0.9334 (mmp) REVERT: E 431 MET cc_start: 0.9861 (OUTLIER) cc_final: 0.9305 (mmm) REVERT: E 435 THR cc_start: 0.9630 (OUTLIER) cc_final: 0.8869 (p) REVERT: E 478 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.9070 (ptm) REVERT: E 519 MET cc_start: 0.9609 (ttp) cc_final: 0.9338 (mmp) REVERT: F 145 MET cc_start: 0.8205 (mtp) cc_final: 0.7927 (ptp) REVERT: G 431 MET cc_start: 0.9857 (OUTLIER) cc_final: 0.9333 (mmm) REVERT: G 478 MET cc_start: 0.9342 (ptm) cc_final: 0.9087 (ptm) REVERT: G 519 MET cc_start: 0.9621 (ttp) cc_final: 0.9343 (mmp) REVERT: H 145 MET cc_start: 0.8237 (mtp) cc_final: 0.7958 (ptp) outliers start: 28 outliers final: 22 residues processed: 135 average time/residue: 0.1314 time to fit residues: 31.7877 Evaluate side-chains 147 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain G residue 431 MET Chi-restraints excluded: chain G residue 435 THR Chi-restraints excluded: chain G residue 448 ILE Chi-restraints excluded: chain G residue 620 VAL Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 5 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 118 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.030952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.028053 restraints weight = 296089.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.028513 restraints weight = 188964.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.028854 restraints weight = 137204.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.029011 restraints weight = 110468.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.029212 restraints weight = 99582.563| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 25272 Z= 0.098 Angle : 0.589 12.539 34596 Z= 0.278 Chirality : 0.039 0.168 4100 Planarity : 0.003 0.055 4404 Dihedral : 3.946 15.226 3596 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.88 % Allowed : 14.54 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.15), residues: 3340 helix: 2.62 (0.12), residues: 1944 sheet: -0.97 (0.37), residues: 156 loop : -0.70 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 493 TYR 0.013 0.001 TYR A 71 PHE 0.017 0.001 PHE E 69 TRP 0.016 0.001 TRP A 370 HIS 0.002 0.001 HIS E 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (25268) covalent geometry : angle 0.58882 / 0.28 (34584) hydrogen bonds : bond 0.02644 / 1.82 ( 1504) hydrogen bonds : angle 3.71431 / 2.75 ( 4380) link_NAG-ASN : bond 0.00003 / 0.00 ( 4) link_NAG-ASN : angle 0.99025 / 0.46 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3288.84 seconds wall clock time: 58 minutes 14.45 seconds (3494.45 seconds total)