Starting phenix.real_space_refine on Mon Jul 28 06:57:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cfs_30346/07_2025/7cfs_30346.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cfs_30346/07_2025/7cfs_30346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cfs_30346/07_2025/7cfs_30346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cfs_30346/07_2025/7cfs_30346.map" model { file = "/net/cci-nas-00/data/ceres_data/7cfs_30346/07_2025/7cfs_30346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cfs_30346/07_2025/7cfs_30346.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians S 81 5.16 5 Na 1 4.78 5 C 6402 2.51 5 N 1631 2.21 5 O 1859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9974 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3249 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3267 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 407} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3268 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' NA': 1, 'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.35, per 1000 atoms: 0.64 Number of scatterers: 9974 At special positions: 0 Unit cell: (97.344, 96.33, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 81 16.00 Na 1 11.00 O 1859 8.00 N 1631 7.00 C 6402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.33 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.33 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.02 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.33 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 395 " " NAG A 602 " - " ASN A 368 " " NAG B 601 " - " ASN B 395 " " NAG B 602 " - " ASN B 368 " " NAG C 601 " - " ASN C 395 " " NAG C 602 " - " ASN C 368 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 35.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 45 through 61 removed outlier: 4.264A pdb=" N LEU A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.511A pdb=" N HIS A 70 " --> pdb=" O TYR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.830A pdb=" N VAL A 103 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.543A pdb=" N HIS A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 140 removed outlier: 3.581A pdb=" N ILE A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.706A pdb=" N ARG A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.583A pdb=" N ASP A 183 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 184' Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.810A pdb=" N TYR A 229 " --> pdb=" O GLN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.559A pdb=" N TYR A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.784A pdb=" N LYS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.548A pdb=" N PHE A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.620A pdb=" N ALA A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.513A pdb=" N GLY A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 443 removed outlier: 4.012A pdb=" N GLY A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 462 removed outlier: 3.822A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 61 removed outlier: 4.263A pdb=" N LEU B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.509A pdb=" N HIS B 70 " --> pdb=" O TYR B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.830A pdb=" N VAL B 103 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 removed outlier: 3.542A pdb=" N HIS B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 140 removed outlier: 3.582A pdb=" N ILE B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.707A pdb=" N ARG B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.582A pdb=" N ASP B 183 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 184 " --> pdb=" O ALA B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 184' Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.810A pdb=" N TYR B 229 " --> pdb=" O GLN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.559A pdb=" N TYR B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.784A pdb=" N LYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.548A pdb=" N PHE B 352 " --> pdb=" O PRO B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 394 removed outlier: 3.620A pdb=" N ALA B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.513A pdb=" N GLY B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 443 removed outlier: 4.012A pdb=" N GLY B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 462 removed outlier: 3.822A pdb=" N LEU B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 4.263A pdb=" N LEU C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.510A pdb=" N HIS C 70 " --> pdb=" O TYR C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.830A pdb=" N VAL C 103 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.543A pdb=" N HIS C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.581A pdb=" N ILE C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU C 138 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.707A pdb=" N ARG C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 180 through 184 removed outlier: 3.583A pdb=" N ASP C 183 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 184 " --> pdb=" O ALA C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 184' Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.811A pdb=" N TYR C 229 " --> pdb=" O GLN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.560A pdb=" N TYR C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.783A pdb=" N LYS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.547A pdb=" N PHE C 352 " --> pdb=" O PRO C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 394 removed outlier: 3.620A pdb=" N ALA C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.513A pdb=" N GLY C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 443 removed outlier: 4.013A pdb=" N GLY C 433 " --> pdb=" O ALA C 429 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 462 removed outlier: 3.822A pdb=" N LEU C 451 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR C 458 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS C 462 " --> pdb=" O TYR C 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 81 removed outlier: 10.264A pdb=" N PHE A 269 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N ILE A 410 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR A 271 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE A 412 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL A 273 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL A 414 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS A 275 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN A 416 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 277 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 274 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 276 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 278 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 223 removed outlier: 10.264A pdb=" N PHE A 269 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N ILE A 410 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR A 271 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE A 412 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL A 273 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL A 414 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS A 275 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN A 416 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 277 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 189 removed outlier: 7.261A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 250 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 81 removed outlier: 10.264A pdb=" N PHE B 269 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE B 410 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR B 271 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE B 412 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL B 273 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL B 414 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS B 275 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN B 416 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU B 277 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 274 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 276 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 278 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 221 through 223 removed outlier: 10.264A pdb=" N PHE B 269 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE B 410 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR B 271 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE B 412 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL B 273 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL B 414 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS B 275 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN B 416 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU B 277 " --> pdb=" O ASN B 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 185 through 189 removed outlier: 7.262A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B 250 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 81 removed outlier: 10.264A pdb=" N PHE C 269 " --> pdb=" O LEU C 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE C 410 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR C 271 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE C 412 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N VAL C 273 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL C 414 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS C 275 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN C 416 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU C 277 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 274 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 276 " --> pdb=" O GLY C 373 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 278 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 221 through 223 removed outlier: 10.264A pdb=" N PHE C 269 " --> pdb=" O LEU C 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE C 410 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR C 271 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE C 412 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N VAL C 273 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL C 414 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS C 275 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN C 416 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU C 277 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB5, first strand: chain 'C' and resid 185 through 189 removed outlier: 7.262A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 250 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 174 303 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3154 1.34 - 1.45: 1745 1.45 - 1.57: 5202 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 10209 Sorted by residual: bond pdb=" CAI Y01 B 603 " pdb=" CAK Y01 B 603 " ideal model delta sigma weight residual 1.492 1.386 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" CAI Y01 C 603 " pdb=" CAK Y01 C 603 " ideal model delta sigma weight residual 1.492 1.386 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" CAI Y01 A 603 " pdb=" CAK Y01 A 603 " ideal model delta sigma weight residual 1.492 1.387 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" CAI Y01 C 603 " pdb=" CAZ Y01 C 603 " ideal model delta sigma weight residual 1.332 1.380 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" CAI Y01 A 603 " pdb=" CAZ Y01 A 603 " ideal model delta sigma weight residual 1.332 1.380 -0.048 2.00e-02 2.50e+03 5.78e+00 ... (remaining 10204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 13283 1.94 - 3.88: 492 3.88 - 5.82: 65 5.82 - 7.76: 21 7.76 - 9.70: 21 Bond angle restraints: 13882 Sorted by residual: angle pdb=" N ILE A 381 " pdb=" CA ILE A 381 " pdb=" C ILE A 381 " ideal model delta sigma weight residual 108.88 117.02 -8.14 2.16e+00 2.14e-01 1.42e+01 angle pdb=" N ILE C 381 " pdb=" CA ILE C 381 " pdb=" C ILE C 381 " ideal model delta sigma weight residual 108.88 116.98 -8.10 2.16e+00 2.14e-01 1.41e+01 angle pdb=" N ILE B 381 " pdb=" CA ILE B 381 " pdb=" C ILE B 381 " ideal model delta sigma weight residual 108.88 116.97 -8.09 2.16e+00 2.14e-01 1.40e+01 angle pdb=" CA ILE C 381 " pdb=" C ILE C 381 " pdb=" N PRO C 382 " ideal model delta sigma weight residual 118.88 124.19 -5.31 1.54e+00 4.22e-01 1.19e+01 angle pdb=" CA ILE B 381 " pdb=" C ILE B 381 " pdb=" N PRO B 382 " ideal model delta sigma weight residual 118.88 124.17 -5.29 1.54e+00 4.22e-01 1.18e+01 ... (remaining 13877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 5486 16.89 - 33.78: 656 33.78 - 50.68: 141 50.68 - 67.57: 39 67.57 - 84.46: 21 Dihedral angle restraints: 6343 sinusoidal: 2607 harmonic: 3736 Sorted by residual: dihedral pdb=" CB CYS C 323 " pdb=" SG CYS C 323 " pdb=" SG CYS C 345 " pdb=" CB CYS C 345 " ideal model delta sinusoidal sigma weight residual -86.00 -170.46 84.46 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS B 323 " pdb=" SG CYS B 323 " pdb=" SG CYS B 345 " pdb=" CB CYS B 345 " ideal model delta sinusoidal sigma weight residual -86.00 -170.45 84.45 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A 323 " pdb=" SG CYS A 323 " pdb=" SG CYS A 345 " pdb=" CB CYS A 345 " ideal model delta sinusoidal sigma weight residual -86.00 -170.45 84.45 1 1.00e+01 1.00e-02 8.67e+01 ... (remaining 6340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1248 0.067 - 0.135: 270 0.135 - 0.202: 33 0.202 - 0.270: 0 0.270 - 0.337: 6 Chirality restraints: 1557 Sorted by residual: chirality pdb=" CBG Y01 C 603 " pdb=" CAQ Y01 C 603 " pdb=" CBD Y01 C 603 " pdb=" CBI Y01 C 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CBG Y01 B 603 " pdb=" CAQ Y01 B 603 " pdb=" CBD Y01 B 603 " pdb=" CBI Y01 B 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CBG Y01 A 603 " pdb=" CAQ Y01 A 603 " pdb=" CBD Y01 A 603 " pdb=" CBI Y01 A 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.66 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 1554 not shown) Planarity restraints: 1795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 338 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO B 339 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 338 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 339 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 338 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO C 339 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 339 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 339 " -0.026 5.00e-02 4.00e+02 ... (remaining 1792 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 25 2.45 - 3.06: 5484 3.06 - 3.67: 14301 3.67 - 4.29: 20002 4.29 - 4.90: 33905 Nonbonded interactions: 73717 Sorted by model distance: nonbonded pdb=" CE1 HIS C 73 " pdb=" OE1 GLN C 422 " model vdw 1.835 3.260 nonbonded pdb=" ND1 HIS C 73 " pdb=" OE1 GLN C 422 " model vdw 1.971 3.120 nonbonded pdb=" CD2 HIS A 73 " pdb=" OE1 GLN A 422 " model vdw 1.990 3.260 nonbonded pdb=" CD2 HIS B 73 " pdb=" OE1 GLN B 422 " model vdw 2.116 3.260 nonbonded pdb=" OD1 ASP A 434 " pdb="NA NA A 604 " model vdw 2.251 2.470 ... (remaining 73712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 87 or (resid 88 through 89 and (name N or name \ CA or name C or name O or name CB )) or resid 90 through 198 or (resid 199 and ( \ name N or name CA or name C or name O or name CB )) or resid 200 through 290 or \ (resid 291 through 300 and (name N or name CA or name C or name O or name CB )) \ or resid 301 through 452 or (resid 453 through 455 and (name N or name CA or nam \ e C or name O or name CB )) or resid 456 through 464 or (resid 465 and (name N o \ r name CA or name C or name O or name CB )) or resid 601 through 603)) selection = (chain 'B' and (resid 40 through 42 or (resid 43 through 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 146 or (resid 147 throu \ gh 148 and (name N or name CA or name C or name O or name CB )) or resid 149 thr \ ough 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) \ or resid 183 through 290 or (resid 291 through 300 and (name N or name CA or nam \ e C or name O or name CB )) or resid 301 through 314 or (resid 315 and (name N o \ r name CA or name C or name O or name CB )) or resid 316 through 363 or (resid 3 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 365 through \ 452 or (resid 453 through 455 and (name N or name CA or name C or name O or nam \ e CB )) or resid 456 through 465 or resid 601 through 603)) selection = (chain 'C' and (resid 40 through 87 or (resid 88 through 89 and (name N or name \ CA or name C or name O or name CB )) or resid 90 through 146 or (resid 147 throu \ gh 148 and (name N or name CA or name C or name O or name CB )) or resid 149 thr \ ough 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) \ or resid 183 through 198 or (resid 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 234 or (resid 235 and (name N or name CA or \ name C or name O or name CB )) or resid 236 through 314 or (resid 315 and (name \ N or name CA or name C or name O or name CB )) or resid 316 through 363 or (res \ id 364 and (name N or name CA or name C or name O or name CB )) or resid 365 thr \ ough 457 or (resid 458 through 459 and (name N or name CA or name C or name O or \ name CB )) or resid 460 through 465 or resid 601 through 603)) } 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.410 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.009 0.299 10236 Z= 0.426 Angle : 1.090 34.509 13942 Z= 0.548 Chirality : 0.058 0.337 1557 Planarity : 0.005 0.047 1789 Dihedral : 15.513 84.427 3880 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.60 % Allowed : 8.97 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.35 (0.18), residues: 1272 helix: -4.61 (0.10), residues: 342 sheet: -3.63 (0.23), residues: 300 loop : -2.77 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 46 HIS 0.004 0.001 HIS B 329 PHE 0.018 0.002 PHE B 263 TYR 0.016 0.001 TYR C 426 ARG 0.003 0.000 ARG A 371 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 6) link_NAG-ASN : angle 3.27069 ( 18) hydrogen bonds : bond 0.30271 ( 294) hydrogen bonds : angle 10.91542 ( 810) SS BOND : bond 0.11288 ( 21) SS BOND : angle 9.99785 ( 42) covalent geometry : bond 0.00761 (10209) covalent geometry : angle 0.93645 (13882) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 1.154 Fit side-chains REVERT: A 50 PHE cc_start: 0.8789 (t80) cc_final: 0.8562 (t80) REVERT: A 219 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6821 (mt-10) REVERT: A 313 ASP cc_start: 0.8171 (t70) cc_final: 0.7848 (t0) REVERT: A 327 MET cc_start: 0.8442 (mtp) cc_final: 0.8171 (mtm) REVERT: A 330 MET cc_start: 0.9331 (mtt) cc_final: 0.8551 (mtt) REVERT: A 342 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.7043 (t80) REVERT: A 351 ASP cc_start: 0.8245 (t0) cc_final: 0.7928 (t0) REVERT: B 291 LYS cc_start: 0.8194 (tppt) cc_final: 0.7774 (tttp) REVERT: B 313 ASP cc_start: 0.8265 (t70) cc_final: 0.8018 (t0) REVERT: B 330 MET cc_start: 0.9270 (mtt) cc_final: 0.8499 (mtt) REVERT: B 342 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8499 (t80) REVERT: C 63 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7203 (tm-30) REVERT: C 313 ASP cc_start: 0.8246 (t70) cc_final: 0.7835 (t0) REVERT: C 330 MET cc_start: 0.9240 (mtt) cc_final: 0.8682 (mtt) REVERT: C 342 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.7071 (t80) outliers start: 6 outliers final: 0 residues processed: 188 average time/residue: 0.2658 time to fit residues: 66.5505 Evaluate side-chains 134 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain C residue 342 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 73 HIS A 276 GLN A 329 HIS ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN B 73 HIS B 276 GLN B 438 GLN C 276 GLN C 329 HIS ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.159164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114580 restraints weight = 13179.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.118160 restraints weight = 7443.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120332 restraints weight = 5488.957| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10236 Z= 0.125 Angle : 0.576 7.463 13942 Z= 0.294 Chirality : 0.041 0.128 1557 Planarity : 0.004 0.035 1789 Dihedral : 6.724 57.833 1727 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.92 % Allowed : 15.02 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.20), residues: 1272 helix: -2.75 (0.20), residues: 372 sheet: -3.37 (0.25), residues: 276 loop : -2.00 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 46 HIS 0.006 0.001 HIS B 73 PHE 0.017 0.001 PHE A 301 TYR 0.018 0.001 TYR C 67 ARG 0.003 0.000 ARG A 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 6) link_NAG-ASN : angle 2.18956 ( 18) hydrogen bonds : bond 0.03318 ( 294) hydrogen bonds : angle 5.86756 ( 810) SS BOND : bond 0.00154 ( 21) SS BOND : angle 1.37883 ( 42) covalent geometry : bond 0.00295 (10209) covalent geometry : angle 0.56726 (13882) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.216 Fit side-chains REVERT: A 63 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7571 (tm-30) REVERT: A 313 ASP cc_start: 0.7545 (t70) cc_final: 0.7249 (t0) REVERT: A 327 MET cc_start: 0.8461 (mtp) cc_final: 0.8242 (mtm) REVERT: A 330 MET cc_start: 0.9388 (mtt) cc_final: 0.8683 (mtt) REVERT: A 342 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.7142 (t80) REVERT: A 351 ASP cc_start: 0.7908 (t0) cc_final: 0.7626 (t0) REVERT: A 421 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7975 (mt-10) REVERT: B 291 LYS cc_start: 0.8258 (tppt) cc_final: 0.7816 (tttp) REVERT: B 313 ASP cc_start: 0.7568 (t70) cc_final: 0.7123 (t0) REVERT: B 330 MET cc_start: 0.9360 (mtt) cc_final: 0.8612 (mtt) REVERT: B 342 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8605 (t80) REVERT: C 211 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8022 (mtpp) REVERT: C 233 TRP cc_start: 0.8038 (p90) cc_final: 0.7699 (p90) REVERT: C 313 ASP cc_start: 0.7507 (t70) cc_final: 0.7159 (t0) REVERT: C 330 MET cc_start: 0.9311 (mtt) cc_final: 0.8761 (mtt) REVERT: C 342 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.7164 (t80) REVERT: C 351 ASP cc_start: 0.7961 (t0) cc_final: 0.7739 (t0) REVERT: C 421 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7587 (tt0) outliers start: 19 outliers final: 9 residues processed: 177 average time/residue: 0.1968 time to fit residues: 51.2052 Evaluate side-chains 146 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 86 optimal weight: 4.9990 chunk 10 optimal weight: 0.0270 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS C 66 GLN C 110 HIS C 438 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.162392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116876 restraints weight = 13308.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120479 restraints weight = 7590.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122598 restraints weight = 5639.010| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10236 Z= 0.094 Angle : 0.528 7.615 13942 Z= 0.268 Chirality : 0.040 0.129 1557 Planarity : 0.003 0.034 1789 Dihedral : 6.101 57.514 1727 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.52 % Allowed : 17.24 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.22), residues: 1272 helix: -1.76 (0.24), residues: 375 sheet: -2.93 (0.27), residues: 276 loop : -1.57 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 46 HIS 0.001 0.000 HIS C 73 PHE 0.013 0.001 PHE C 301 TYR 0.016 0.001 TYR C 67 ARG 0.007 0.000 ARG C 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 6) link_NAG-ASN : angle 1.94959 ( 18) hydrogen bonds : bond 0.02667 ( 294) hydrogen bonds : angle 5.42013 ( 810) SS BOND : bond 0.00196 ( 21) SS BOND : angle 1.41889 ( 42) covalent geometry : bond 0.00218 (10209) covalent geometry : angle 0.51873 (13882) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.9394 (mtt) cc_final: 0.8631 (mtt) REVERT: A 342 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.7116 (t80) REVERT: A 351 ASP cc_start: 0.8006 (t0) cc_final: 0.7781 (t0) REVERT: B 291 LYS cc_start: 0.8260 (tppt) cc_final: 0.8014 (ttmt) REVERT: B 327 MET cc_start: 0.8442 (mtp) cc_final: 0.8156 (mtp) REVERT: B 330 MET cc_start: 0.9365 (mtt) cc_final: 0.8533 (mtt) REVERT: B 342 TYR cc_start: 0.9065 (OUTLIER) cc_final: 0.8562 (t80) REVERT: B 399 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7651 (tm-30) REVERT: C 211 LYS cc_start: 0.8448 (mtmt) cc_final: 0.8011 (mtpp) REVERT: C 313 ASP cc_start: 0.7474 (t70) cc_final: 0.7182 (t0) REVERT: C 342 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.7111 (t80) REVERT: C 351 ASP cc_start: 0.8144 (t0) cc_final: 0.7884 (t0) REVERT: C 421 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7671 (tt0) outliers start: 25 outliers final: 9 residues processed: 162 average time/residue: 0.2045 time to fit residues: 51.7150 Evaluate side-chains 146 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 82 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS C 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.158732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115161 restraints weight = 13162.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116929 restraints weight = 7722.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117923 restraints weight = 6133.113| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10236 Z= 0.167 Angle : 0.571 8.731 13942 Z= 0.289 Chirality : 0.041 0.128 1557 Planarity : 0.003 0.035 1789 Dihedral : 6.060 59.174 1727 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.23 % Allowed : 19.25 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.23), residues: 1272 helix: -0.99 (0.27), residues: 375 sheet: -2.71 (0.27), residues: 300 loop : -1.62 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 46 HIS 0.002 0.001 HIS A 73 PHE 0.011 0.001 PHE C 442 TYR 0.013 0.001 TYR C 67 ARG 0.004 0.000 ARG C 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00023 ( 6) link_NAG-ASN : angle 2.15886 ( 18) hydrogen bonds : bond 0.02819 ( 294) hydrogen bonds : angle 5.24683 ( 810) SS BOND : bond 0.00322 ( 21) SS BOND : angle 1.62639 ( 42) covalent geometry : bond 0.00399 (10209) covalent geometry : angle 0.55949 (13882) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 327 MET cc_start: 0.8180 (mtt) cc_final: 0.7299 (mtp) REVERT: A 330 MET cc_start: 0.9419 (mtt) cc_final: 0.8482 (mtt) REVERT: A 342 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.7028 (t80) REVERT: A 351 ASP cc_start: 0.8276 (t0) cc_final: 0.7972 (t0) REVERT: B 179 CYS cc_start: 0.6456 (OUTLIER) cc_final: 0.6076 (m) REVERT: B 291 LYS cc_start: 0.8213 (tppt) cc_final: 0.7975 (ttmt) REVERT: B 327 MET cc_start: 0.8515 (mtp) cc_final: 0.8190 (mtp) REVERT: B 330 MET cc_start: 0.9400 (mtt) cc_final: 0.8551 (mtt) REVERT: B 342 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.8584 (t80) REVERT: B 345 CYS cc_start: 0.5611 (m) cc_final: 0.5346 (m) REVERT: B 351 ASP cc_start: 0.8080 (t0) cc_final: 0.7814 (t0) REVERT: B 399 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7738 (tm-30) REVERT: C 211 LYS cc_start: 0.8475 (mtmt) cc_final: 0.8053 (mtpp) REVERT: C 313 ASP cc_start: 0.7557 (t70) cc_final: 0.7272 (t0) REVERT: C 330 MET cc_start: 0.9461 (mtt) cc_final: 0.8697 (mtt) REVERT: C 342 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.7003 (t80) REVERT: C 351 ASP cc_start: 0.8370 (t0) cc_final: 0.8051 (t0) outliers start: 32 outliers final: 18 residues processed: 158 average time/residue: 0.1736 time to fit residues: 43.0361 Evaluate side-chains 153 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 114 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 GLN C 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114506 restraints weight = 13054.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118029 restraints weight = 7406.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120123 restraints weight = 5480.396| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10236 Z= 0.128 Angle : 0.537 7.365 13942 Z= 0.269 Chirality : 0.040 0.130 1557 Planarity : 0.003 0.040 1789 Dihedral : 5.808 59.867 1727 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.33 % Allowed : 19.05 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.24), residues: 1272 helix: -0.81 (0.27), residues: 393 sheet: -2.63 (0.28), residues: 282 loop : -1.37 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 46 HIS 0.002 0.000 HIS A 73 PHE 0.012 0.001 PHE C 442 TYR 0.011 0.001 TYR B 417 ARG 0.003 0.000 ARG C 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00043 ( 6) link_NAG-ASN : angle 2.02990 ( 18) hydrogen bonds : bond 0.02471 ( 294) hydrogen bonds : angle 5.12794 ( 810) SS BOND : bond 0.00266 ( 21) SS BOND : angle 1.38967 ( 42) covalent geometry : bond 0.00307 (10209) covalent geometry : angle 0.52746 (13882) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8218 (mm) REVERT: A 327 MET cc_start: 0.8088 (mtt) cc_final: 0.7136 (mtp) REVERT: A 330 MET cc_start: 0.9398 (mtt) cc_final: 0.8538 (mtt) REVERT: A 342 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.7000 (t80) REVERT: A 351 ASP cc_start: 0.7902 (t0) cc_final: 0.7664 (t0) REVERT: B 291 LYS cc_start: 0.8289 (tppt) cc_final: 0.8070 (ttmt) REVERT: B 327 MET cc_start: 0.8530 (mtp) cc_final: 0.8209 (mtp) REVERT: B 330 MET cc_start: 0.9353 (mtt) cc_final: 0.8532 (mtt) REVERT: B 342 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.8537 (t80) REVERT: B 351 ASP cc_start: 0.7815 (t0) cc_final: 0.7609 (t0) REVERT: B 399 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7728 (tm-30) REVERT: C 211 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8070 (mtpp) REVERT: C 313 ASP cc_start: 0.7364 (t70) cc_final: 0.7137 (t0) REVERT: C 330 MET cc_start: 0.9408 (mtt) cc_final: 0.8755 (mtt) REVERT: C 342 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.6806 (t80) REVERT: C 351 ASP cc_start: 0.7986 (t0) cc_final: 0.7785 (t0) outliers start: 43 outliers final: 31 residues processed: 169 average time/residue: 0.2115 time to fit residues: 55.5745 Evaluate side-chains 170 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 378 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 0.0470 overall best weight: 0.8480 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.160255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115968 restraints weight = 13104.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119531 restraints weight = 7412.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121661 restraints weight = 5478.149| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10236 Z= 0.100 Angle : 0.516 7.511 13942 Z= 0.259 Chirality : 0.040 0.189 1557 Planarity : 0.003 0.042 1789 Dihedral : 5.624 58.731 1727 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.54 % Allowed : 19.66 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.25), residues: 1272 helix: -0.82 (0.26), residues: 414 sheet: -2.56 (0.30), residues: 258 loop : -1.09 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 46 HIS 0.001 0.000 HIS C 73 PHE 0.011 0.001 PHE C 442 TYR 0.012 0.001 TYR C 417 ARG 0.003 0.000 ARG C 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00073 ( 6) link_NAG-ASN : angle 1.88915 ( 18) hydrogen bonds : bond 0.02277 ( 294) hydrogen bonds : angle 5.01881 ( 810) SS BOND : bond 0.00247 ( 21) SS BOND : angle 1.50222 ( 42) covalent geometry : bond 0.00239 (10209) covalent geometry : angle 0.50573 (13882) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8154 (mm) REVERT: A 327 MET cc_start: 0.7934 (mtt) cc_final: 0.7017 (mtp) REVERT: A 330 MET cc_start: 0.9415 (mtt) cc_final: 0.8526 (mtt) REVERT: A 342 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.6943 (t80) REVERT: A 351 ASP cc_start: 0.7984 (t0) cc_final: 0.7782 (t0) REVERT: A 400 TYR cc_start: 0.8369 (t80) cc_final: 0.8028 (t80) REVERT: B 46 TRP cc_start: 0.8114 (OUTLIER) cc_final: 0.7368 (m100) REVERT: B 291 LYS cc_start: 0.8289 (tppt) cc_final: 0.8053 (ttmt) REVERT: B 327 MET cc_start: 0.8484 (mtp) cc_final: 0.8147 (mtp) REVERT: B 330 MET cc_start: 0.9364 (mtt) cc_final: 0.8501 (mtt) REVERT: B 342 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8676 (t80) REVERT: B 351 ASP cc_start: 0.7979 (t0) cc_final: 0.7767 (t0) REVERT: B 399 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7732 (tm-30) REVERT: C 58 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8110 (mm) REVERT: C 211 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8063 (mtpp) REVERT: C 313 ASP cc_start: 0.7409 (t70) cc_final: 0.7194 (t0) REVERT: C 330 MET cc_start: 0.9418 (mtt) cc_final: 0.8755 (mtt) REVERT: C 342 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.6770 (t80) REVERT: C 421 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7743 (tt0) outliers start: 45 outliers final: 28 residues processed: 186 average time/residue: 0.1591 time to fit residues: 45.7500 Evaluate side-chains 173 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 75 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 107 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 93 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.171678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.130328 restraints weight = 13150.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132047 restraints weight = 10270.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133536 restraints weight = 7318.884| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10236 Z= 0.090 Angle : 0.507 6.858 13942 Z= 0.253 Chirality : 0.040 0.234 1557 Planarity : 0.003 0.056 1789 Dihedral : 5.546 59.329 1727 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.73 % Allowed : 20.97 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.25), residues: 1272 helix: -0.71 (0.26), residues: 417 sheet: -2.61 (0.29), residues: 279 loop : -0.94 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 233 HIS 0.003 0.000 HIS C 329 PHE 0.009 0.001 PHE C 442 TYR 0.011 0.001 TYR A 417 ARG 0.002 0.000 ARG C 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 6) link_NAG-ASN : angle 1.79874 ( 18) hydrogen bonds : bond 0.02159 ( 294) hydrogen bonds : angle 4.96386 ( 810) SS BOND : bond 0.00215 ( 21) SS BOND : angle 1.39356 ( 42) covalent geometry : bond 0.00218 (10209) covalent geometry : angle 0.49813 (13882) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 CYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5659 (m) REVERT: A 327 MET cc_start: 0.7843 (mtt) cc_final: 0.7590 (mtt) REVERT: A 330 MET cc_start: 0.9299 (mtt) cc_final: 0.8477 (mtt) REVERT: A 342 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.7006 (t80) REVERT: A 345 CYS cc_start: 0.5154 (m) cc_final: 0.4837 (m) REVERT: A 400 TYR cc_start: 0.8367 (t80) cc_final: 0.8027 (t80) REVERT: B 46 TRP cc_start: 0.8175 (OUTLIER) cc_final: 0.7407 (m100) REVERT: B 330 MET cc_start: 0.9252 (mtt) cc_final: 0.8402 (mtt) REVERT: B 342 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.8537 (t80) REVERT: B 399 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7657 (tm-30) REVERT: C 58 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8006 (mm) REVERT: C 63 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7388 (tm-30) REVERT: C 211 LYS cc_start: 0.8390 (mtmt) cc_final: 0.8059 (mtpp) REVERT: C 342 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.6761 (t80) REVERT: C 345 CYS cc_start: 0.5194 (m) cc_final: 0.4715 (m) REVERT: C 421 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7694 (tt0) outliers start: 37 outliers final: 25 residues processed: 174 average time/residue: 0.1653 time to fit residues: 44.1588 Evaluate side-chains 166 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 24 optimal weight: 0.6980 chunk 72 optimal weight: 0.3980 chunk 113 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.164995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123466 restraints weight = 13086.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124680 restraints weight = 7320.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125471 restraints weight = 5618.575| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10236 Z= 0.109 Angle : 0.531 8.421 13942 Z= 0.260 Chirality : 0.041 0.229 1557 Planarity : 0.003 0.044 1789 Dihedral : 5.524 59.386 1727 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.03 % Allowed : 21.77 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.25), residues: 1272 helix: -0.55 (0.27), residues: 417 sheet: -2.58 (0.30), residues: 270 loop : -0.87 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 233 HIS 0.002 0.000 HIS C 73 PHE 0.009 0.001 PHE C 442 TYR 0.011 0.001 TYR A 417 ARG 0.002 0.000 ARG C 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 6) link_NAG-ASN : angle 1.87386 ( 18) hydrogen bonds : bond 0.02364 ( 294) hydrogen bonds : angle 4.94187 ( 810) SS BOND : bond 0.00213 ( 21) SS BOND : angle 1.25484 ( 42) covalent geometry : bond 0.00264 (10209) covalent geometry : angle 0.52360 (13882) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 CYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5660 (m) REVERT: A 327 MET cc_start: 0.7821 (mtt) cc_final: 0.6932 (mtp) REVERT: A 330 MET cc_start: 0.9312 (mtt) cc_final: 0.8378 (mtt) REVERT: A 342 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.6906 (t80) REVERT: A 345 CYS cc_start: 0.5245 (m) cc_final: 0.4955 (m) REVERT: B 46 TRP cc_start: 0.8233 (OUTLIER) cc_final: 0.7399 (m100) REVERT: B 238 GLU cc_start: 0.7727 (pp20) cc_final: 0.7173 (tm-30) REVERT: B 291 LYS cc_start: 0.8495 (ttmt) cc_final: 0.8282 (ttmt) REVERT: B 327 MET cc_start: 0.8334 (mtt) cc_final: 0.7974 (mtt) REVERT: B 330 MET cc_start: 0.9295 (mtt) cc_final: 0.8401 (mtt) REVERT: B 342 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8522 (t80) REVERT: B 399 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7699 (tm-30) REVERT: C 58 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7955 (mm) REVERT: C 63 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7397 (tm-30) REVERT: C 211 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8092 (mtpp) REVERT: C 342 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.6891 (t80) REVERT: C 345 CYS cc_start: 0.5501 (m) cc_final: 0.5051 (m) REVERT: C 421 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7729 (tt0) outliers start: 40 outliers final: 29 residues processed: 167 average time/residue: 0.1605 time to fit residues: 41.6125 Evaluate side-chains 169 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 378 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 116 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 81 optimal weight: 0.0040 chunk 103 optimal weight: 8.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.170199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.128091 restraints weight = 13122.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.130471 restraints weight = 8829.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132172 restraints weight = 5875.524| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10236 Z= 0.123 Angle : 0.532 8.365 13942 Z= 0.265 Chirality : 0.042 0.303 1557 Planarity : 0.003 0.061 1789 Dihedral : 5.556 59.545 1727 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.83 % Allowed : 22.58 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.25), residues: 1272 helix: -0.48 (0.26), residues: 408 sheet: -2.57 (0.30), residues: 270 loop : -0.89 (0.28), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 233 HIS 0.002 0.000 HIS A 329 PHE 0.008 0.001 PHE C 442 TYR 0.011 0.001 TYR B 417 ARG 0.002 0.000 ARG C 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00034 ( 6) link_NAG-ASN : angle 1.95583 ( 18) hydrogen bonds : bond 0.02384 ( 294) hydrogen bonds : angle 4.95283 ( 810) SS BOND : bond 0.00221 ( 21) SS BOND : angle 1.24572 ( 42) covalent geometry : bond 0.00302 (10209) covalent geometry : angle 0.52441 (13882) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 291 LYS cc_start: 0.8227 (tppt) cc_final: 0.7955 (ttpt) REVERT: A 327 MET cc_start: 0.7850 (mtt) cc_final: 0.6976 (mtp) REVERT: A 330 MET cc_start: 0.9247 (mtt) cc_final: 0.8336 (mtt) REVERT: A 342 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.6956 (t80) REVERT: B 46 TRP cc_start: 0.8171 (OUTLIER) cc_final: 0.7293 (m100) REVERT: B 238 GLU cc_start: 0.7680 (pp20) cc_final: 0.7146 (tm-30) REVERT: B 327 MET cc_start: 0.8317 (mtt) cc_final: 0.8038 (mtt) REVERT: B 330 MET cc_start: 0.9232 (mtt) cc_final: 0.8418 (mtt) REVERT: B 342 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8506 (t80) REVERT: B 345 CYS cc_start: 0.4719 (m) cc_final: 0.4378 (m) REVERT: B 399 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7741 (tm-30) REVERT: C 58 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8043 (mm) REVERT: C 63 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7271 (tm-30) REVERT: C 211 LYS cc_start: 0.8411 (mtmt) cc_final: 0.8107 (mtpp) REVERT: C 330 MET cc_start: 0.9204 (mtt) cc_final: 0.8865 (mtt) REVERT: C 342 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.6825 (t80) outliers start: 38 outliers final: 29 residues processed: 159 average time/residue: 0.1796 time to fit residues: 44.0550 Evaluate side-chains 164 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 46 TRP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 378 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.161586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117221 restraints weight = 13252.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120937 restraints weight = 7343.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123144 restraints weight = 5364.436| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10236 Z= 0.101 Angle : 0.528 8.346 13942 Z= 0.258 Chirality : 0.041 0.294 1557 Planarity : 0.004 0.061 1789 Dihedral : 5.436 58.774 1727 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.73 % Allowed : 22.98 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.25), residues: 1272 helix: -0.40 (0.27), residues: 420 sheet: -2.46 (0.30), residues: 270 loop : -0.81 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 233 HIS 0.002 0.000 HIS C 329 PHE 0.007 0.001 PHE B 442 TYR 0.010 0.001 TYR A 417 ARG 0.002 0.000 ARG C 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00079 ( 6) link_NAG-ASN : angle 1.87147 ( 18) hydrogen bonds : bond 0.02202 ( 294) hydrogen bonds : angle 4.86252 ( 810) SS BOND : bond 0.00196 ( 21) SS BOND : angle 1.20019 ( 42) covalent geometry : bond 0.00245 (10209) covalent geometry : angle 0.52025 (13882) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 327 MET cc_start: 0.7816 (mtt) cc_final: 0.7550 (mtt) REVERT: A 330 MET cc_start: 0.9234 (mtt) cc_final: 0.8366 (mtt) REVERT: A 342 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.6928 (t80) REVERT: B 46 TRP cc_start: 0.8203 (OUTLIER) cc_final: 0.7188 (m100) REVERT: B 238 GLU cc_start: 0.7559 (pp20) cc_final: 0.7113 (tm-30) REVERT: B 330 MET cc_start: 0.9203 (mtt) cc_final: 0.8451 (mtt) REVERT: B 342 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.8565 (t80) REVERT: B 345 CYS cc_start: 0.4495 (m) cc_final: 0.4164 (m) REVERT: B 399 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7712 (tm-30) REVERT: C 63 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7353 (tm-30) REVERT: C 211 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8107 (mtpp) REVERT: C 330 MET cc_start: 0.9226 (mtt) cc_final: 0.8885 (mtt) REVERT: C 342 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.6785 (t80) REVERT: C 421 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7725 (tt0) outliers start: 37 outliers final: 29 residues processed: 160 average time/residue: 0.1992 time to fit residues: 49.3666 Evaluate side-chains 164 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 46 TRP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 93 optimal weight: 0.0020 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.161890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.118272 restraints weight = 13063.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121923 restraints weight = 7279.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124073 restraints weight = 5345.632| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10236 Z= 0.090 Angle : 0.516 8.031 13942 Z= 0.252 Chirality : 0.041 0.293 1557 Planarity : 0.003 0.060 1789 Dihedral : 5.363 58.710 1727 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.83 % Allowed : 22.78 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.25), residues: 1272 helix: -0.27 (0.26), residues: 432 sheet: -2.42 (0.30), residues: 273 loop : -0.74 (0.30), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 233 HIS 0.002 0.000 HIS C 329 PHE 0.007 0.001 PHE C 98 TYR 0.010 0.001 TYR A 417 ARG 0.002 0.000 ARG C 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00110 ( 6) link_NAG-ASN : angle 1.76639 ( 18) hydrogen bonds : bond 0.02118 ( 294) hydrogen bonds : angle 4.82875 ( 810) SS BOND : bond 0.00170 ( 21) SS BOND : angle 1.17940 ( 42) covalent geometry : bond 0.00218 (10209) covalent geometry : angle 0.50947 (13882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3370.17 seconds wall clock time: 61 minutes 27.52 seconds (3687.52 seconds total)