Starting phenix.real_space_refine on Fri Sep 19 09:57:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5k7l_8215/09_2025/5k7l_8215.cif Found real_map, /net/cci-nas-00/data/ceres_data/5k7l_8215/09_2025/5k7l_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 { model { file = "/net/cci-nas-00/data/ceres_data/5k7l_8215/09_2025/5k7l_8215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5k7l_8215/09_2025/5k7l_8215.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5k7l_8215/09_2025/5k7l_8215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5k7l_8215/09_2025/5k7l_8215.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 18 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: 5.87, per 1000 atoms: 0.24 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: 2.34 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.86 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: 4.95 Time building geometry restraints manager: 3.17 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: 13076 13.29 - 26.58: 1200 26.58 - 39.87: 480 39.87 - 53.16: 108 53.16 - 66.45: 24 Dihedral angle restraints: 14888 sinusoidal: 5012 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 14885 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: 0.08 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: 1.570 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: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.520 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 13.100 66.453 8488 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 aren 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 covalent geometry : bond 0.00765 (25268) covalent geometry : angle 1.36264 (34584) hydrogen bonds : bond 0.16584 ( 1504) hydrogen bonds : angle 5.51885 ( 4380) link_NAG-ASN : bond 0.00214 ( 4) link_NAG-ASN : angle 2.74950 ( 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 : 0.957 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: 0.1577 time to fit residues: 44.7538 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 : 0.989 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.033408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.028706 restraints weight = 378316.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.029190 restraints weight = 224621.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.029512 restraints weight = 157220.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.029775 restraints weight = 121536.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.029932 restraints weight = 101133.102| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 25272 Z= 0.238 Angle : 0.630 7.082 34596 Z= 0.339 Chirality : 0.040 0.144 4100 Planarity : 0.004 0.050 4404 Dihedral : 4.785 24.036 3880 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.41 % Allowed : 10.54 % Favored : 88.05 % 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 aren not related in a simple way. whole: 1.18 (0.15), residues: 3340 helix: 2.44 (0.12), residues: 2000 sheet: -2.62 (0.28), residues: 220 loop : -1.69 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 387 TYR 0.017 0.002 TYR G 44 PHE 0.019 0.002 PHE A 241 TRP 0.019 0.002 TRP E 370 HIS 0.005 0.001 HIS C 643 Details of bonding type rmsd covalent geometry : bond 0.00471 (25268) covalent geometry : angle 0.62807 (34584) hydrogen bonds : bond 0.03879 ( 1504) hydrogen bonds : angle 4.17839 ( 4380) link_NAG-ASN : bond 0.01158 ( 4) link_NAG-ASN : angle 2.38026 ( 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 : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.9585 (ttp) cc_final: 0.9264 (mmp) REVERT: A 568 MET cc_start: 0.9360 (mmm) cc_final: 0.8926 (mmm) REVERT: B 145 MET cc_start: 0.8503 (mmm) cc_final: 0.8203 (mtp) REVERT: C 431 MET cc_start: 0.9686 (tpt) cc_final: 0.9134 (tpp) REVERT: C 519 MET cc_start: 0.9566 (ttp) cc_final: 0.9258 (mmp) REVERT: C 568 MET cc_start: 0.9362 (mmm) cc_final: 0.8927 (mmm) REVERT: D 145 MET cc_start: 0.8478 (mmm) cc_final: 0.8192 (mtp) REVERT: E 431 MET cc_start: 0.9684 (tpt) cc_final: 0.9133 (tpp) REVERT: E 519 MET cc_start: 0.9564 (ttp) cc_final: 0.9258 (mmp) REVERT: E 568 MET cc_start: 0.9364 (mmm) cc_final: 0.8930 (mmm) REVERT: F 145 MET cc_start: 0.8459 (mmm) cc_final: 0.8184 (mtp) REVERT: G 431 MET cc_start: 0.9692 (tpt) cc_final: 0.9145 (tpp) REVERT: G 519 MET cc_start: 0.9579 (ttp) cc_final: 0.9264 (mmp) REVERT: G 568 MET cc_start: 0.9362 (mmm) cc_final: 0.8927 (mmm) REVERT: H 145 MET cc_start: 0.8474 (mmm) cc_final: 0.8190 (mtp) outliers start: 32 outliers final: 8 residues processed: 144 average time/residue: 0.1407 time to fit residues: 35.0242 Evaluate side-chains 126 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 352 LEU Chi-restraints excluded: chain H residue 144 MET 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: 0.0050 chunk 276 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 280 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 297 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.038798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.035195 restraints weight = 216944.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.035556 restraints weight = 164600.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.035582 restraints weight = 126619.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.035582 restraints weight = 124550.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.035582 restraints weight = 124550.712| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25272 Z= 0.150 Angle : 0.538 7.890 34596 Z= 0.282 Chirality : 0.039 0.194 4100 Planarity : 0.004 0.054 4404 Dihedral : 4.236 17.109 3880 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.41 % Allowed : 12.21 % Favored : 86.38 % 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 aren not related in a simple way. whole: 1.55 (0.16), residues: 3340 helix: 2.64 (0.12), residues: 2000 sheet: -2.39 (0.27), residues: 232 loop : -1.33 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 387 TYR 0.012 0.001 TYR C 464 PHE 0.017 0.001 PHE A 359 TRP 0.016 0.001 TRP G 370 HIS 0.002 0.001 HIS A 574 Details of bonding type rmsd covalent geometry : bond 0.00310 (25268) covalent geometry : angle 0.53790 (34584) hydrogen bonds : bond 0.03310 ( 1504) hydrogen bonds : angle 3.89539 ( 4380) link_NAG-ASN : bond 0.00448 ( 4) link_NAG-ASN : angle 1.30530 ( 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 156 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.983 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: 0.9238 (OUTLIER) cc_final: 0.8711 (m-80) REVERT: A 488 MET cc_start: 0.9237 (tmm) cc_final: 0.9024 (ppp) REVERT: A 519 MET cc_start: 0.9710 (ttp) cc_final: 0.9285 (mmp) REVERT: A 568 MET cc_start: 0.9470 (mmm) cc_final: 0.9127 (mmm) REVERT: C 269 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8676 (m-80) REVERT: C 431 MET cc_start: 0.9620 (tpt) cc_final: 0.9414 (tpp) REVERT: C 488 MET cc_start: 0.9235 (tmm) cc_final: 0.9024 (ppp) REVERT: C 519 MET cc_start: 0.9709 (ttp) cc_final: 0.9278 (mmp) REVERT: C 568 MET cc_start: 0.9461 (mmm) cc_final: 0.9118 (mmm) REVERT: E 269 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8720 (m-80) REVERT: E 431 MET cc_start: 0.9617 (tpt) cc_final: 0.9411 (tpp) REVERT: E 488 MET cc_start: 0.9239 (tmm) cc_final: 0.9031 (ppp) REVERT: E 519 MET cc_start: 0.9740 (ttp) cc_final: 0.9291 (mmp) REVERT: E 568 MET cc_start: 0.9452 (mmm) cc_final: 0.9111 (mmm) REVERT: G 269 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8741 (m-80) REVERT: G 478 MET cc_start: 0.9410 (OUTLIER) cc_final: 0.9170 (ptm) REVERT: G 488 MET cc_start: 0.9242 (tmm) cc_final: 0.9035 (ppp) REVERT: G 519 MET cc_start: 0.9732 (ttp) cc_final: 0.9292 (mmp) REVERT: G 568 MET cc_start: 0.9460 (mmm) cc_final: 0.9112 (mmm) outliers start: 32 outliers final: 11 residues processed: 148 average time/residue: 0.1290 time to fit residues: 33.7935 Evaluate side-chains 139 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 PHE 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 269 PHE 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 269 PHE 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 269 PHE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 13 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 281 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 40.0000 chunk 194 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.031855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.028789 restraints weight = 284402.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.029244 restraints weight = 184240.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.029622 restraints weight = 129178.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.029807 restraints weight = 103672.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.029939 restraints weight = 92693.011| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25272 Z= 0.127 Angle : 0.516 10.409 34596 Z= 0.264 Chirality : 0.038 0.187 4100 Planarity : 0.003 0.054 4404 Dihedral : 3.997 16.166 3880 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.45 % Allowed : 10.81 % Favored : 87.74 % 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 aren not related in a simple way. whole: 1.71 (0.16), residues: 3340 helix: 2.73 (0.12), residues: 1968 sheet: -2.25 (0.27), residues: 232 loop : -1.07 (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 241 TRP 0.014 0.001 TRP G 370 HIS 0.002 0.001 HIS G 643 Details of bonding type rmsd covalent geometry : bond 0.00264 (25268) covalent geometry : angle 0.51548 (34584) hydrogen bonds : bond 0.02949 ( 1504) hydrogen bonds : angle 3.71676 ( 4380) link_NAG-ASN : bond 0.00399 ( 4) link_NAG-ASN : angle 1.24285 ( 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 163 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.043 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: 0.9157 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: A 435 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8806 (p) REVERT: A 519 MET cc_start: 0.9798 (ttp) cc_final: 0.9320 (mmp) REVERT: A 560 ASP cc_start: 0.9403 (OUTLIER) cc_final: 0.8800 (t0) REVERT: C 269 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8652 (m-80) REVERT: C 431 MET cc_start: 0.9688 (tpt) cc_final: 0.9424 (tpp) REVERT: C 519 MET cc_start: 0.9796 (ttp) cc_final: 0.9318 (mmp) REVERT: C 560 ASP cc_start: 0.9402 (OUTLIER) cc_final: 0.8795 (t0) REVERT: E 269 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8650 (m-80) REVERT: E 431 MET cc_start: 0.9693 (tpt) cc_final: 0.9402 (tpp) REVERT: E 435 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.8899 (p) REVERT: E 519 MET cc_start: 0.9796 (ttp) cc_final: 0.9314 (mmp) REVERT: E 560 ASP cc_start: 0.9406 (OUTLIER) cc_final: 0.8804 (t0) REVERT: G 269 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8652 (m-80) REVERT: G 366 MET cc_start: 0.9651 (mmm) cc_final: 0.9209 (mpp) REVERT: G 457 MET cc_start: 0.9177 (ptm) cc_final: 0.8956 (ptm) REVERT: G 519 MET cc_start: 0.9798 (ttp) cc_final: 0.9317 (mmp) REVERT: G 560 ASP cc_start: 0.9408 (OUTLIER) cc_final: 0.8807 (t0) outliers start: 33 outliers final: 11 residues processed: 148 average time/residue: 0.1350 time to fit residues: 35.2087 Evaluate side-chains 144 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 560 ASP 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 478 MET Chi-restraints excluded: chain C residue 560 ASP 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 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 478 MET Chi-restraints excluded: chain G residue 560 ASP Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 312 optimal weight: 6.9990 chunk 333 optimal weight: 8.9990 chunk 190 optimal weight: 0.9980 chunk 267 optimal weight: 0.6980 chunk 309 optimal weight: 0.5980 chunk 189 optimal weight: 0.1980 chunk 72 optimal weight: 50.0000 chunk 325 optimal weight: 0.0040 chunk 97 optimal weight: 20.0000 chunk 314 optimal weight: 0.0770 chunk 211 optimal weight: 2.9990 overall best weight: 0.3150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.039767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.036006 restraints weight = 202596.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.036325 restraints weight = 156544.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.036326 restraints weight = 116739.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.036326 restraints weight = 116659.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.036326 restraints weight = 116659.604| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3227 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= 0.092 Angle : 0.539 10.813 34596 Z= 0.261 Chirality : 0.038 0.205 4100 Planarity : 0.003 0.055 4404 Dihedral : 3.738 15.731 3880 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.36 % Allowed : 11.60 % Favored : 87.04 % 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 aren not related in a simple way. whole: 1.73 (0.15), residues: 3340 helix: 2.75 (0.12), residues: 1936 sheet: -2.05 (0.28), residues: 232 loop : -0.99 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 84 TYR 0.011 0.001 TYR C 464 PHE 0.016 0.001 PHE B 141 TRP 0.014 0.001 TRP E 370 HIS 0.001 0.000 HIS E 583 Details of bonding type rmsd covalent geometry : bond 0.00194 (25268) covalent geometry : angle 0.53915 (34584) hydrogen bonds : bond 0.02683 ( 1504) hydrogen bonds : angle 3.57670 ( 4380) link_NAG-ASN : bond 0.00040 ( 4) link_NAG-ASN : angle 1.08607 ( 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 154 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8708 (m-80) REVERT: A 435 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8972 (p) REVERT: A 519 MET cc_start: 0.9710 (ttp) cc_final: 0.9255 (mmp) REVERT: A 560 ASP cc_start: 0.9234 (OUTLIER) cc_final: 0.8511 (t0) REVERT: B 145 MET cc_start: 0.8140 (mtp) cc_final: 0.7849 (ptp) REVERT: C 269 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8689 (m-80) REVERT: C 431 MET cc_start: 0.9698 (tpt) cc_final: 0.9409 (tpp) REVERT: C 435 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.8936 (p) REVERT: C 478 MET cc_start: 0.9334 (ptm) cc_final: 0.9111 (tmm) REVERT: C 519 MET cc_start: 0.9724 (ttp) cc_final: 0.9260 (mmp) REVERT: C 560 ASP cc_start: 0.9225 (OUTLIER) cc_final: 0.8503 (t0) REVERT: D 145 MET cc_start: 0.8184 (mtp) cc_final: 0.7887 (ptp) REVERT: E 269 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8722 (m-80) REVERT: E 431 MET cc_start: 0.9682 (tpt) cc_final: 0.9418 (tpp) REVERT: E 478 MET cc_start: 0.9328 (ptm) cc_final: 0.9113 (tmm) REVERT: E 519 MET cc_start: 0.9734 (ttp) cc_final: 0.9264 (mmp) REVERT: E 560 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.8504 (t0) REVERT: F 145 MET cc_start: 0.8141 (mtp) cc_final: 0.7851 (ptp) REVERT: G 269 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8744 (m-80) REVERT: G 366 MET cc_start: 0.9609 (mmm) cc_final: 0.9346 (mpp) REVERT: G 435 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8963 (p) REVERT: G 478 MET cc_start: 0.9334 (ptm) cc_final: 0.9117 (tmm) REVERT: G 519 MET cc_start: 0.9719 (ttp) cc_final: 0.9259 (mmp) REVERT: G 560 ASP cc_start: 0.9236 (OUTLIER) cc_final: 0.8515 (t0) REVERT: H 145 MET cc_start: 0.8107 (mtp) cc_final: 0.7821 (ptp) outliers start: 31 outliers final: 8 residues processed: 150 average time/residue: 0.1241 time to fit residues: 32.9106 Evaluate side-chains 139 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 435 THR 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 435 THR 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 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 435 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 321 optimal weight: 10.0000 chunk 183 optimal weight: 0.0370 chunk 196 optimal weight: 6.9990 chunk 303 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 252 optimal weight: 4.9990 chunk 287 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 316 optimal weight: 10.0000 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 583 HIS C 93 ASN C 583 HIS E 93 ASN E 583 HIS G 93 ASN G 583 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.031489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.028442 restraints weight = 287445.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.028857 restraints weight = 184097.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.029255 restraints weight = 139785.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.029402 restraints weight = 112007.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.029554 restraints weight = 101837.092| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25272 Z= 0.172 Angle : 0.565 10.569 34596 Z= 0.280 Chirality : 0.039 0.242 4100 Planarity : 0.003 0.055 4404 Dihedral : 3.821 15.689 3880 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.27 % Allowed : 11.82 % Favored : 86.91 % 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 aren not related in a simple way. whole: 1.91 (0.16), residues: 3340 helix: 2.84 (0.12), residues: 1960 sheet: -2.08 (0.27), residues: 232 loop : -0.86 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 387 TYR 0.014 0.001 TYR G 71 PHE 0.020 0.001 PHE A 69 TRP 0.011 0.001 TRP E 370 HIS 0.003 0.001 HIS G 574 Details of bonding type rmsd covalent geometry : bond 0.00345 (25268) covalent geometry : angle 0.56494 (34584) hydrogen bonds : bond 0.02788 ( 1504) hydrogen bonds : angle 3.62992 ( 4380) link_NAG-ASN : bond 0.00592 ( 4) link_NAG-ASN : angle 1.28577 ( 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 156 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8620 (m-80) REVERT: A 435 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8860 (p) REVERT: A 519 MET cc_start: 0.9788 (ttp) cc_final: 0.9333 (mmp) REVERT: A 560 ASP cc_start: 0.9423 (OUTLIER) cc_final: 0.8864 (t0) REVERT: A 568 MET cc_start: 0.9256 (mmm) cc_final: 0.8802 (mmm) REVERT: B 145 MET cc_start: 0.8406 (mtp) cc_final: 0.8065 (ptp) REVERT: C 269 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8624 (m-80) REVERT: C 431 MET cc_start: 0.9755 (tpt) cc_final: 0.9308 (mmm) REVERT: C 435 THR cc_start: 0.9390 (OUTLIER) cc_final: 0.8839 (t) REVERT: C 519 MET cc_start: 0.9783 (ttp) cc_final: 0.9333 (mmp) REVERT: C 560 ASP cc_start: 0.9420 (OUTLIER) cc_final: 0.8859 (t0) REVERT: C 568 MET cc_start: 0.9260 (mmm) cc_final: 0.8804 (mmm) REVERT: D 145 MET cc_start: 0.8410 (mtp) cc_final: 0.8068 (ptp) REVERT: E 269 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8633 (m-80) REVERT: E 431 MET cc_start: 0.9762 (tpt) cc_final: 0.9311 (mmm) REVERT: E 435 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.8833 (t) REVERT: E 519 MET cc_start: 0.9785 (ttp) cc_final: 0.9332 (mmp) REVERT: E 560 ASP cc_start: 0.9423 (OUTLIER) cc_final: 0.8861 (t0) REVERT: E 568 MET cc_start: 0.9266 (mmm) cc_final: 0.8808 (mmm) REVERT: F 145 MET cc_start: 0.8402 (mtp) cc_final: 0.8061 (ptp) REVERT: G 269 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8637 (m-80) REVERT: G 435 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8961 (p) REVERT: G 519 MET cc_start: 0.9788 (ttp) cc_final: 0.9333 (mmp) REVERT: G 560 ASP cc_start: 0.9427 (OUTLIER) cc_final: 0.8871 (t0) REVERT: G 568 MET cc_start: 0.9254 (mmm) cc_final: 0.8801 (mmm) REVERT: H 145 MET cc_start: 0.8397 (mtp) cc_final: 0.8055 (ptp) outliers start: 29 outliers final: 12 residues processed: 147 average time/residue: 0.1263 time to fit residues: 32.1267 Evaluate side-chains 147 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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 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 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 435 THR 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: 20.0000 chunk 254 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 311 optimal weight: 10.0000 chunk 195 optimal weight: 8.9990 chunk 331 optimal weight: 20.0000 chunk 273 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 HIS ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 HIS ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 HIS G 85 GLN ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 708 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.030650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.027607 restraints weight = 303837.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.028024 restraints weight = 193147.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.028373 restraints weight = 146776.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.028631 restraints weight = 117760.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.028727 restraints weight = 101049.673| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25272 Z= 0.213 Angle : 0.602 11.484 34596 Z= 0.304 Chirality : 0.039 0.252 4100 Planarity : 0.004 0.056 4404 Dihedral : 4.192 18.956 3880 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.70 % Allowed : 12.57 % Favored : 86.73 % 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 aren not related in a simple way. whole: 1.65 (0.15), residues: 3340 helix: 2.55 (0.12), residues: 1960 sheet: -2.15 (0.27), residues: 236 loop : -0.81 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 387 TYR 0.011 0.002 TYR C 44 PHE 0.031 0.002 PHE C 69 TRP 0.012 0.002 TRP G 370 HIS 0.004 0.001 HIS A 574 Details of bonding type rmsd covalent geometry : bond 0.00419 (25268) covalent geometry : angle 0.60154 (34584) hydrogen bonds : bond 0.03130 ( 1504) hydrogen bonds : angle 3.79908 ( 4380) link_NAG-ASN : bond 0.00733 ( 4) link_NAG-ASN : angle 1.27582 ( 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 135 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9108 (mmm) cc_final: 0.8511 (mmm) REVERT: A 435 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.9037 (p) REVERT: A 519 MET cc_start: 0.9737 (ttp) cc_final: 0.9346 (mmp) REVERT: B 145 MET cc_start: 0.8344 (mtp) cc_final: 0.7995 (ptp) REVERT: C 61 MET cc_start: 0.9152 (mmm) cc_final: 0.8531 (mmm) REVERT: C 431 MET cc_start: 0.9823 (OUTLIER) cc_final: 0.9271 (mmm) REVERT: C 435 THR cc_start: 0.9520 (OUTLIER) cc_final: 0.8900 (t) REVERT: C 478 MET cc_start: 0.9381 (ptm) cc_final: 0.9175 (ptm) REVERT: C 519 MET cc_start: 0.9729 (ttp) cc_final: 0.9343 (mmp) REVERT: D 145 MET cc_start: 0.8347 (mtp) cc_final: 0.7997 (ptp) REVERT: E 61 MET cc_start: 0.9146 (mmm) cc_final: 0.8525 (mmm) REVERT: E 431 MET cc_start: 0.9830 (tpt) cc_final: 0.9280 (mmm) REVERT: E 435 THR cc_start: 0.9542 (OUTLIER) cc_final: 0.8930 (t) REVERT: E 478 MET cc_start: 0.9368 (ptm) cc_final: 0.9165 (ptm) REVERT: E 519 MET cc_start: 0.9736 (ttp) cc_final: 0.9347 (mmp) REVERT: F 145 MET cc_start: 0.8331 (mtp) cc_final: 0.7984 (ptp) REVERT: G 61 MET cc_start: 0.9098 (mmm) cc_final: 0.8505 (mmm) REVERT: G 366 MET cc_start: 0.9597 (mmm) cc_final: 0.9222 (mpp) REVERT: G 435 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9088 (p) REVERT: G 478 MET cc_start: 0.9371 (ptm) cc_final: 0.9169 (ptm) REVERT: G 519 MET cc_start: 0.9739 (ttp) cc_final: 0.9348 (mmp) REVERT: H 145 MET cc_start: 0.8338 (mtp) cc_final: 0.7990 (ptp) outliers start: 16 outliers final: 7 residues processed: 127 average time/residue: 0.1253 time to fit residues: 28.2949 Evaluate side-chains 128 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 144 MET 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 D residue 144 MET Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 435 THR 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 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: 5.9990 chunk 0 optimal weight: 20.0000 chunk 222 optimal weight: 20.0000 chunk 315 optimal weight: 7.9990 chunk 246 optimal weight: 40.0000 chunk 24 optimal weight: 5.9990 chunk 317 optimal weight: 8.9990 chunk 306 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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 = 0.3034 r_free = 0.3034 target = 0.030662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.027672 restraints weight = 299322.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.028056 restraints weight = 193028.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.028410 restraints weight = 146429.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.028636 restraints weight = 117205.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.028685 restraints weight = 102558.657| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25272 Z= 0.166 Angle : 0.570 10.706 34596 Z= 0.282 Chirality : 0.039 0.213 4100 Planarity : 0.003 0.055 4404 Dihedral : 4.109 19.885 3880 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.01 % Allowed : 13.31 % Favored : 85.68 % 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 aren not related in a simple way. whole: 1.76 (0.15), residues: 3340 helix: 2.68 (0.12), residues: 1940 sheet: -2.19 (0.29), residues: 228 loop : -0.77 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 387 TYR 0.014 0.001 TYR E 100 PHE 0.026 0.001 PHE E 69 TRP 0.014 0.001 TRP E 370 HIS 0.002 0.001 HIS G 574 Details of bonding type rmsd covalent geometry : bond 0.00331 (25268) covalent geometry : angle 0.57007 (34584) hydrogen bonds : bond 0.02863 ( 1504) hydrogen bonds : angle 3.77335 ( 4380) link_NAG-ASN : bond 0.00526 ( 4) link_NAG-ASN : angle 0.96608 ( 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 142 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8527 (tpt) cc_final: 0.8233 (tpp) REVERT: A 478 MET cc_start: 0.9355 (tmm) cc_final: 0.8902 (ppp) REVERT: A 519 MET cc_start: 0.9740 (ttp) cc_final: 0.9330 (mmp) REVERT: A 568 MET cc_start: 0.9400 (mmm) cc_final: 0.8868 (mmm) REVERT: B 145 MET cc_start: 0.8443 (mtp) cc_final: 0.8096 (ptp) REVERT: C 99 MET cc_start: 0.8572 (tpt) cc_final: 0.8273 (tpp) REVERT: C 431 MET cc_start: 0.9813 (OUTLIER) cc_final: 0.9327 (mmm) REVERT: C 435 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.8913 (t) REVERT: C 478 MET cc_start: 0.9313 (ptm) cc_final: 0.9095 (ptm) REVERT: C 519 MET cc_start: 0.9727 (ttp) cc_final: 0.9323 (mmp) REVERT: C 568 MET cc_start: 0.9410 (mmm) cc_final: 0.8879 (mmm) REVERT: D 145 MET cc_start: 0.8448 (mtp) cc_final: 0.8098 (ptp) REVERT: E 99 MET cc_start: 0.8582 (tpt) cc_final: 0.8279 (tpp) REVERT: E 431 MET cc_start: 0.9815 (OUTLIER) cc_final: 0.9332 (mmm) REVERT: E 435 THR cc_start: 0.9479 (OUTLIER) cc_final: 0.8920 (t) REVERT: E 478 MET cc_start: 0.9299 (ptm) cc_final: 0.9083 (ptm) REVERT: E 519 MET cc_start: 0.9732 (ttp) cc_final: 0.9324 (mmp) REVERT: E 568 MET cc_start: 0.9411 (mmm) cc_final: 0.8884 (mmm) REVERT: F 145 MET cc_start: 0.8435 (mtp) cc_final: 0.8088 (ptp) REVERT: G 99 MET cc_start: 0.8522 (tpt) cc_final: 0.8228 (tpp) REVERT: G 366 MET cc_start: 0.9615 (mmm) cc_final: 0.9245 (mpp) REVERT: G 478 MET cc_start: 0.9306 (ptm) cc_final: 0.9090 (ptm) REVERT: G 519 MET cc_start: 0.9740 (ttp) cc_final: 0.9328 (mmp) REVERT: G 568 MET cc_start: 0.9409 (mmm) cc_final: 0.8875 (mmm) REVERT: H 145 MET cc_start: 0.8440 (mtp) cc_final: 0.8093 (ptp) outliers start: 23 outliers final: 13 residues processed: 135 average time/residue: 0.1229 time to fit residues: 29.5346 Evaluate side-chains 136 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 620 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 248 VAL 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 431 MET Chi-restraints excluded: chain E residue 435 THR 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 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: 9.9990 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 0.0070 chunk 185 optimal weight: 20.0000 chunk 229 optimal weight: 20.0000 chunk 306 optimal weight: 0.0170 chunk 10 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 234 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 85 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.031075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.028099 restraints weight = 294547.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.028515 restraints weight = 188946.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.028898 restraints weight = 143166.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.029068 restraints weight = 114134.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.029221 restraints weight = 102356.195| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25272 Z= 0.113 Angle : 0.557 11.416 34596 Z= 0.269 Chirality : 0.038 0.187 4100 Planarity : 0.003 0.055 4404 Dihedral : 3.950 19.066 3880 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.97 % Allowed : 13.14 % Favored : 85.90 % 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 aren not related in a simple way. whole: 1.91 (0.15), residues: 3340 helix: 2.79 (0.12), residues: 1936 sheet: -2.08 (0.29), residues: 228 loop : -0.68 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 537 TYR 0.010 0.001 TYR C 371 PHE 0.020 0.001 PHE G 69 TRP 0.014 0.001 TRP E 370 HIS 0.002 0.001 HIS G 574 Details of bonding type rmsd covalent geometry : bond 0.00237 (25268) covalent geometry : angle 0.55713 (34584) hydrogen bonds : bond 0.02643 ( 1504) hydrogen bonds : angle 3.63059 ( 4380) link_NAG-ASN : bond 0.00258 ( 4) link_NAG-ASN : angle 0.89672 ( 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 143 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.863 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 99 MET cc_start: 0.8675 (tpt) cc_final: 0.8217 (tpp) REVERT: A 287 ILE cc_start: 0.9572 (OUTLIER) cc_final: 0.9254 (pt) REVERT: A 475 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.8900 (t80) REVERT: A 478 MET cc_start: 0.9317 (tmm) cc_final: 0.8759 (ppp) REVERT: A 568 MET cc_start: 0.9371 (mmm) cc_final: 0.8821 (mmm) REVERT: C 99 MET cc_start: 0.8711 (tpt) cc_final: 0.8255 (tpp) REVERT: C 287 ILE cc_start: 0.9574 (OUTLIER) cc_final: 0.9260 (pt) REVERT: C 431 MET cc_start: 0.9807 (OUTLIER) cc_final: 0.9284 (mmm) REVERT: C 478 MET cc_start: 0.9291 (ptm) cc_final: 0.9070 (ptm) REVERT: C 568 MET cc_start: 0.9374 (mmm) cc_final: 0.8828 (mmm) REVERT: E 99 MET cc_start: 0.8702 (tpt) cc_final: 0.8249 (tpp) REVERT: E 287 ILE cc_start: 0.9583 (OUTLIER) cc_final: 0.9264 (pt) REVERT: E 366 MET cc_start: 0.9608 (mmm) cc_final: 0.9245 (mpp) REVERT: E 431 MET cc_start: 0.9797 (OUTLIER) cc_final: 0.9256 (mmm) REVERT: E 478 MET cc_start: 0.9277 (ptm) cc_final: 0.9060 (ptm) REVERT: E 568 MET cc_start: 0.9377 (mmm) cc_final: 0.8828 (mmm) REVERT: G 99 MET cc_start: 0.8656 (tpt) cc_final: 0.8202 (tpp) REVERT: G 287 ILE cc_start: 0.9575 (OUTLIER) cc_final: 0.9256 (pt) REVERT: G 366 MET cc_start: 0.9648 (mmm) cc_final: 0.9259 (mpp) REVERT: G 478 MET cc_start: 0.9280 (ptm) cc_final: 0.9064 (ptm) REVERT: G 568 MET cc_start: 0.9369 (mmm) cc_final: 0.8821 (mmm) outliers start: 22 outliers final: 15 residues processed: 136 average time/residue: 0.1245 time to fit residues: 30.1027 Evaluate side-chains 140 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 475 PHE 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 287 ILE 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 287 ILE Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain E residue 435 THR 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 287 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: 10.0000 chunk 315 optimal weight: 3.9990 chunk 321 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 275 optimal weight: 20.0000 chunk 206 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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 = 0.030871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.027801 restraints weight = 295419.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.028211 restraints weight = 197639.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.028568 restraints weight = 150698.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.028831 restraints weight = 120922.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.028902 restraints weight = 103873.526| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25272 Z= 0.147 Angle : 0.561 11.130 34596 Z= 0.275 Chirality : 0.038 0.177 4100 Planarity : 0.003 0.055 4404 Dihedral : 3.960 19.407 3880 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.79 % Allowed : 13.71 % Favored : 85.50 % 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 aren not related in a simple way. whole: 1.97 (0.15), residues: 3340 helix: 2.75 (0.12), residues: 1944 sheet: -2.07 (0.34), residues: 184 loop : -0.58 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 387 TYR 0.010 0.001 TYR E 100 PHE 0.021 0.001 PHE G 69 TRP 0.012 0.001 TRP C 370 HIS 0.002 0.001 HIS A 574 Details of bonding type rmsd covalent geometry : bond 0.00298 (25268) covalent geometry : angle 0.56085 (34584) hydrogen bonds : bond 0.02730 ( 1504) hydrogen bonds : angle 3.67684 ( 4380) link_NAG-ASN : bond 0.00443 ( 4) link_NAG-ASN : angle 0.93242 ( 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 137 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.8931 (t80) REVERT: A 478 MET cc_start: 0.9368 (tmm) cc_final: 0.8773 (ppp) REVERT: A 519 MET cc_start: 0.9751 (ttp) cc_final: 0.9328 (mmp) REVERT: A 568 MET cc_start: 0.9399 (mmm) cc_final: 0.8813 (mmm) REVERT: B 145 MET cc_start: 0.8407 (mtp) cc_final: 0.8117 (ptp) REVERT: C 431 MET cc_start: 0.9825 (OUTLIER) cc_final: 0.9269 (mmm) REVERT: C 478 MET cc_start: 0.9317 (ptm) cc_final: 0.9094 (ptm) REVERT: C 519 MET cc_start: 0.9738 (ttp) cc_final: 0.9322 (mmp) REVERT: C 568 MET cc_start: 0.9405 (mmm) cc_final: 0.8821 (mmm) REVERT: D 145 MET cc_start: 0.8405 (mtp) cc_final: 0.8113 (ptp) REVERT: E 431 MET cc_start: 0.9832 (OUTLIER) cc_final: 0.9360 (mmm) REVERT: E 435 THR cc_start: 0.9436 (OUTLIER) cc_final: 0.8803 (t) REVERT: E 478 MET cc_start: 0.9303 (ptm) cc_final: 0.9082 (ptm) REVERT: E 519 MET cc_start: 0.9743 (ttp) cc_final: 0.9322 (mmp) REVERT: E 568 MET cc_start: 0.9410 (mmm) cc_final: 0.8822 (mmm) REVERT: F 145 MET cc_start: 0.8398 (mtp) cc_final: 0.8108 (ptp) REVERT: G 366 MET cc_start: 0.9628 (mmm) cc_final: 0.9246 (mpp) REVERT: G 478 MET cc_start: 0.9304 (ptm) cc_final: 0.9085 (ptm) REVERT: G 519 MET cc_start: 0.9750 (ttp) cc_final: 0.9327 (mmp) REVERT: G 568 MET cc_start: 0.9407 (mmm) cc_final: 0.8816 (mmm) REVERT: H 145 MET cc_start: 0.8408 (mtp) cc_final: 0.8118 (ptp) outliers start: 18 outliers final: 14 residues processed: 130 average time/residue: 0.1263 time to fit residues: 28.9885 Evaluate side-chains 136 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 475 PHE 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 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 431 MET Chi-restraints excluded: chain E residue 435 THR 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 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: 9.9990 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 0.0970 chunk 118 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3036 r_free = 0.3036 target = 0.030704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.027703 restraints weight = 304145.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.028168 restraints weight = 193472.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.028492 restraints weight = 142683.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.028709 restraints weight = 115021.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.028783 restraints weight = 100598.014| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25272 Z= 0.154 Angle : 0.581 11.551 34596 Z= 0.282 Chirality : 0.038 0.166 4100 Planarity : 0.003 0.055 4404 Dihedral : 4.017 21.677 3880 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.14 % Allowed : 13.80 % 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 aren not related in a simple way. whole: 1.99 (0.15), residues: 3340 helix: 2.74 (0.12), residues: 1944 sheet: -2.09 (0.29), residues: 228 loop : -0.43 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 387 TYR 0.009 0.001 TYR E 371 PHE 0.019 0.001 PHE E 69 TRP 0.013 0.001 TRP C 370 HIS 0.003 0.001 HIS C 574 Details of bonding type rmsd covalent geometry : bond 0.00311 (25268) covalent geometry : angle 0.58091 (34584) hydrogen bonds : bond 0.02741 ( 1504) hydrogen bonds : angle 3.70571 ( 4380) link_NAG-ASN : bond 0.00358 ( 4) link_NAG-ASN : angle 0.73731 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3030.97 seconds wall clock time: 53 minutes 43.49 seconds (3223.49 seconds total)