Starting phenix.real_space_refine on Sat Jul 4 03:19:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uaf_26423/07_2026/7uaf_26423.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uaf_26423/07_2026/7uaf_26423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uaf_26423/07_2026/7uaf_26423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uaf_26423/07_2026/7uaf_26423.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uaf_26423/07_2026/7uaf_26423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uaf_26423/07_2026/7uaf_26423.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uaf_26423/07_2026/7uaf_26423.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uaf_26423/07_2026/7uaf_26423.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 Zn 4 6.06 5 S 84 5.16 5 C 11246 2.51 5 N 2979 2.21 5 O 3543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17864 Number of models: 1 Model: "" Number of chains: 22 Chain: "B" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4319 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Chain: "A" Number of atoms: 4313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4313 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4295 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 512} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 4257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4257 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 509} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, ' ZN': 1, 'M6X': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, ' ZN': 1, 'M6X': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, ' ZN': 1, 'M6X': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, ' ZN': 1, 'M6X': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.96, per 1000 atoms: 0.22 Number of scatterers: 17864 At special positions: 0 Unit cell: (110.24, 168.54, 135.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 8 19.99 S 84 16.00 O 3543 8.00 N 2979 7.00 C 11246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 147 " distance=1.99 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS A 308 " distance=2.05 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 431 " distance=2.06 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS B 559 " distance=2.04 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 259 " distance=2.04 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 147 " distance=2.01 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 431 " distance=2.06 Simple disulfide: pdb=" SG CYS A 557 " - pdb=" SG CYS A 559 " distance=2.05 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 259 " distance=2.02 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 147 " distance=2.02 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 431 " distance=2.05 Simple disulfide: pdb=" SG CYS C 557 " - pdb=" SG CYS C 559 " distance=2.05 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 259 " distance=2.04 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 147 " distance=2.01 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 277 " distance=2.04 Simple disulfide: pdb=" SG CYS D 343 " - pdb=" SG CYS D 431 " distance=2.06 Simple disulfide: pdb=" SG CYS D 557 " - pdb=" SG CYS D 559 " distance=2.05 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " NAG I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " BETA1-6 " NAG H 1 " - " FUC H 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG K 1 " - " FUC K 4 " " NAG O 1 " - " FUC O 4 " " NAG R 1 " - " FUC R 4 " NAG-ASN " NAG A 705 " - " ASN A 440 " " NAG B 705 " - " ASN B 440 " " NAG C 705 " - " ASN C 440 " " NAG D 705 " - " ASN D 440 " " NAG E 1 " - " ASN B 140 " " NAG F 1 " - " ASN B 258 " " NAG G 1 " - " ASN B 222 " " NAG H 1 " - " ASN B 414 " " NAG I 1 " - " ASN A 258 " " NAG J 1 " - " ASN A 222 " " NAG K 1 " - " ASN A 414 " " NAG L 1 " - " ASN A 140 " " NAG M 1 " - " ASN C 140 " " NAG N 1 " - " ASN C 222 " " NAG O 1 " - " ASN C 414 " " NAG P 1 " - " ASN D 140 " " NAG Q 1 " - " ASN D 222 " " NAG R 1 " - " ASN D 414 " Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 743.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 165 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 155 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 159 " pdb=" ZN B 703 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 165 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 155 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 159 " pdb=" ZN C 703 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 165 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 155 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 159 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 165 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 155 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 159 " 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3976 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 39 sheets defined 22.8% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 88 through 106 Processing helix chain 'B' and resid 149 through 162 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 180 through 183 Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 232 through 238 Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 440 through 448 removed outlier: 3.505A pdb=" N GLU B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 546 through 551 Processing helix chain 'B' and resid 573 through 578 Processing helix chain 'B' and resid 597 through 600 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 88 through 106 Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.506A pdb=" N SER A 415 " --> pdb=" O PRO A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 448 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 516 through 520 Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'A' and resid 546 through 551 Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 597 through 600 Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.901A pdb=" N ARG C 74 " --> pdb=" O PRO C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 106 Processing helix chain 'C' and resid 149 through 161 Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 171 through 174 Processing helix chain 'C' and resid 180 through 183 removed outlier: 3.651A pdb=" N ILE C 183 " --> pdb=" O TRP C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 183' Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 232 through 238 removed outlier: 3.627A pdb=" N PHE C 235 " --> pdb=" O ILE C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 258 Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 440 through 448 removed outlier: 4.146A pdb=" N GLU C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 497 Processing helix chain 'C' and resid 516 through 520 Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 573 through 577 removed outlier: 3.679A pdb=" N LYS C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 573 through 577' Processing helix chain 'C' and resid 597 through 600 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.527A pdb=" N ARG D 74 " --> pdb=" O PRO D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 106 Processing helix chain 'D' and resid 149 through 162 Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 180 through 183 Processing helix chain 'D' and resid 186 through 192 removed outlier: 4.589A pdb=" N HIS D 189 " --> pdb=" O GLY D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 238 Processing helix chain 'D' and resid 246 through 258 Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 440 through 448 removed outlier: 4.031A pdb=" N GLU D 446 " --> pdb=" O SER D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 520 Processing helix chain 'D' and resid 535 through 539 Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 597 through 600 Processing sheet with id=AA1, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'B' and resid 110 through 112 removed outlier: 7.930A pdb=" N PHE B 122 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 82 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 176 through 178 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 269 Processing sheet with id=AA5, first strand: chain 'B' and resid 265 through 269 removed outlier: 5.801A pdb=" N LEU B 421 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LYS B 349 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASP B 423 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE B 347 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 280 through 281 removed outlier: 6.812A pdb=" N LEU B 358 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR B 379 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 360 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 434 through 438 Processing sheet with id=AA8, first strand: chain 'B' and resid 454 through 455 Processing sheet with id=AA9, first strand: chain 'B' and resid 454 through 455 removed outlier: 3.951A pdb=" N GLY B 466 " --> pdb=" O CYS B 489 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 482 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 569 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 552 through 553 Processing sheet with id=AB2, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AB3, first strand: chain 'A' and resid 110 through 112 removed outlier: 7.940A pdb=" N PHE A 122 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 82 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AB5, first strand: chain 'A' and resid 265 through 269 Processing sheet with id=AB6, first strand: chain 'A' and resid 265 through 269 removed outlier: 5.750A pdb=" N LEU A 421 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LYS A 349 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP A 423 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE A 347 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 280 through 281 removed outlier: 6.777A pdb=" N LEU A 358 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR A 379 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 360 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 434 through 438 Processing sheet with id=AB9, first strand: chain 'A' and resid 454 through 455 Processing sheet with id=AC1, first strand: chain 'A' and resid 454 through 455 removed outlier: 3.983A pdb=" N GLY A 466 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 482 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A 569 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 552 through 553 Processing sheet with id=AC3, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AC4, first strand: chain 'C' and resid 110 through 112 removed outlier: 6.082A pdb=" N ILE C 79 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N PHE C 122 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 82 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AC6, first strand: chain 'C' and resid 265 through 269 Processing sheet with id=AC7, first strand: chain 'C' and resid 265 through 269 removed outlier: 5.721A pdb=" N LEU C 421 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LYS C 349 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP C 423 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE C 347 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 280 through 281 removed outlier: 6.673A pdb=" N LEU C 358 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR C 379 " --> pdb=" O LEU C 358 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL C 360 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 434 through 438 Processing sheet with id=AD1, first strand: chain 'C' and resid 454 through 455 Processing sheet with id=AD2, first strand: chain 'C' and resid 454 through 455 removed outlier: 3.828A pdb=" N GLY C 466 " --> pdb=" O CYS C 489 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE C 571 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU C 484 " --> pdb=" O GLY C 569 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLY C 569 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N PHE C 486 " --> pdb=" O TRP C 567 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TRP C 567 " --> pdb=" O PHE C 486 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL C 488 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N LEU C 565 " --> pdb=" O VAL C 488 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 551 through 553 Processing sheet with id=AD4, first strand: chain 'D' and resid 110 through 112 removed outlier: 8.023A pdb=" N PHE D 122 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE D 82 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 176 through 178 Processing sheet with id=AD6, first strand: chain 'D' and resid 265 through 269 Processing sheet with id=AD7, first strand: chain 'D' and resid 265 through 269 removed outlier: 5.709A pdb=" N LEU D 421 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LYS D 349 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASP D 423 " --> pdb=" O PHE D 347 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE D 347 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 280 through 281 removed outlier: 6.853A pdb=" N LEU D 358 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR D 379 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL D 360 " --> pdb=" O VAL D 377 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 434 through 438 Processing sheet with id=AE1, first strand: chain 'D' and resid 454 through 455 Processing sheet with id=AE2, first strand: chain 'D' and resid 454 through 455 removed outlier: 3.863A pdb=" N GLY D 466 " --> pdb=" O CYS D 489 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU D 482 " --> pdb=" O GLY D 569 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 551 through 553 624 hydrogen bonds defined for protein. 1440 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: 3.08 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4866 1.33 - 1.45: 3929 1.45 - 1.58: 9386 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 18301 Sorted by residual: bond pdb=" C VAL A 300 " pdb=" N ASP A 301 " ideal model delta sigma weight residual 1.328 1.246 0.082 1.40e-02 5.10e+03 3.43e+01 bond pdb=" C ASP C 385 " pdb=" N HIS C 386 " ideal model delta sigma weight residual 1.332 1.263 0.070 1.29e-02 6.01e+03 2.93e+01 bond pdb=" C ASP B 385 " pdb=" N HIS B 386 " ideal model delta sigma weight residual 1.332 1.279 0.054 1.29e-02 6.01e+03 1.74e+01 bond pdb=" C VAL D 300 " pdb=" N ASP D 301 " ideal model delta sigma weight residual 1.330 1.387 -0.057 1.38e-02 5.25e+03 1.72e+01 bond pdb=" C ARG B 579 " pdb=" N SER B 580 " ideal model delta sigma weight residual 1.330 1.272 0.058 1.52e-02 4.33e+03 1.47e+01 ... (remaining 18296 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 17188 1.76 - 3.53: 6310 3.53 - 5.29: 1177 5.29 - 7.06: 146 7.06 - 8.82: 14 Bond angle restraints: 24835 Sorted by residual: angle pdb=" N ARG D 284 " pdb=" CA ARG D 284 " pdb=" C ARG D 284 " ideal model delta sigma weight residual 112.23 104.24 7.99 1.26e+00 6.30e-01 4.02e+01 angle pdb=" C THR C 433 " pdb=" N GLY C 434 " pdb=" CA GLY C 434 " ideal model delta sigma weight residual 121.65 125.87 -4.22 6.80e-01 2.16e+00 3.85e+01 angle pdb=" CA PHE D 590 " pdb=" CB PHE D 590 " pdb=" CG PHE D 590 " ideal model delta sigma weight residual 113.80 119.58 -5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" N ASP D 512 " pdb=" CA ASP D 512 " pdb=" C ASP D 512 " ideal model delta sigma weight residual 109.25 100.43 8.82 1.53e+00 4.27e-01 3.32e+01 angle pdb=" CA ASP C 301 " pdb=" CB ASP C 301 " pdb=" CG ASP C 301 " ideal model delta sigma weight residual 112.60 118.12 -5.52 1.00e+00 1.00e+00 3.05e+01 ... (remaining 24830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 9657 17.90 - 35.80: 669 35.80 - 53.70: 103 53.70 - 71.61: 49 71.61 - 89.51: 18 Dihedral angle restraints: 10496 sinusoidal: 4304 harmonic: 6192 Sorted by residual: dihedral pdb=" CB CYS C 128 " pdb=" SG CYS C 128 " pdb=" SG CYS C 147 " pdb=" CB CYS C 147 " ideal model delta sinusoidal sigma weight residual 93.00 150.93 -57.93 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS D 557 " pdb=" SG CYS D 557 " pdb=" SG CYS D 559 " pdb=" CB CYS D 559 " ideal model delta sinusoidal sigma weight residual -86.00 -143.42 57.42 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS C 557 " pdb=" SG CYS C 557 " pdb=" SG CYS C 559 " pdb=" CB CYS C 559 " ideal model delta sinusoidal sigma weight residual -86.00 -142.55 56.55 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 10493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1667 0.087 - 0.174: 849 0.174 - 0.262: 183 0.262 - 0.349: 42 0.349 - 0.436: 12 Chirality restraints: 2753 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.41e+01 chirality pdb=" C1 FUC H 4 " pdb=" O6 NAG H 1 " pdb=" C2 FUC H 4 " pdb=" O5 FUC H 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.07e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 2.88e+01 ... (remaining 2750 not shown) Planarity restraints: 3192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.319 2.00e-02 2.50e+03 2.75e-01 9.49e+02 pdb=" C7 NAG L 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.020 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.477 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 705 " -0.320 2.00e-02 2.50e+03 2.72e-01 9.22e+02 pdb=" C7 NAG A 705 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A 705 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG A 705 " 0.472 2.00e-02 2.50e+03 pdb=" O7 NAG A 705 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 705 " -0.318 2.00e-02 2.50e+03 2.70e-01 9.10e+02 pdb=" C7 NAG B 705 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG B 705 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG B 705 " 0.469 2.00e-02 2.50e+03 pdb=" O7 NAG B 705 " -0.048 2.00e-02 2.50e+03 ... (remaining 3189 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 38 2.41 - 3.03: 9913 3.03 - 3.65: 25430 3.65 - 4.28: 44391 4.28 - 4.90: 70528 Nonbonded interactions: 150300 Sorted by model distance: nonbonded pdb=" O CYS D 128 " pdb=" O6 M6X D 701 " model vdw 1.783 3.040 nonbonded pdb=" OH TYR B 214 " pdb=" O3 M6X B 701 " model vdw 1.855 3.040 nonbonded pdb=" O CYS D 128 " pdb=" N2 M6X D 701 " model vdw 1.856 3.120 nonbonded pdb=" OD1 ASP B 285 " pdb="CA CA B 702 " model vdw 1.861 2.510 nonbonded pdb=" OH TYR A 214 " pdb=" O3 M6X A 701 " model vdw 1.999 3.040 ... (remaining 150295 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 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 169 or resid 172 through 200 or re \ sid 205 through 259 or (resid 260 through 261 and (name N or name CA or name C o \ r name O or name CB )) or resid 262 through 295 or resid 299 through 332 or (res \ id 333 and (name N or name CA or name C or name O or name CB )) or resid 334 thr \ ough 705)) selection = (chain 'B' and (resid 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 169 or resid 172 through 200 or re \ sid 205 through 259 or (resid 260 through 261 and (name N or name CA or name C o \ r name O or name CB )) or resid 262 through 295 or resid 299 through 332 or (res \ id 333 and (name N or name CA or name C or name O or name CB )) or resid 334 thr \ ough 475 or (resid 476 and (name N or name CA or name C or name O or name CB )) \ or resid 477 through 705)) selection = (chain 'C' and (resid 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 169 or resid 172 through 200 or re \ sid 205 through 259 or (resid 260 through 261 and (name N or name CA or name C o \ r name O or name CB )) or resid 262 through 475 or (resid 476 and (name N or nam \ e CA or name C or name O or name CB )) or resid 477 through 705)) selection = (chain 'D' and (resid 66 through 295 or resid 299 through 475 or (resid 476 and \ (name N or name CA or name C or name O or name CB )) or resid 477 through 705)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'O' selection = chain 'R' } 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 individual isotropic 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.210 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.016 0.509 18376 Z= 0.810 Angle : 1.815 9.623 25003 Z= 1.212 Chirality : 0.105 0.436 2753 Planarity : 0.021 0.275 3174 Dihedral : 13.594 89.507 6457 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.16 % Allowed : 3.11 % Favored : 96.73 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2117 helix: -1.52 (0.27), residues: 259 sheet: 0.67 (0.21), residues: 515 loop : -0.08 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 549 TYR 0.105 0.018 TYR A 313 PHE 0.073 0.012 PHE B 593 TRP 0.138 0.022 TRP A 436 HIS 0.024 0.004 HIS C 573 Details of bonding type rmsd/Z covalent geometry : bond 0.01195 / 0.73 (18301) covalent geometry : angle 1.79964 / 1.21 (24835) SS BOND : bond 0.01858 / 1.12 ( 21) SS BOND : angle 2.32265 / 1.73 ( 42) hydrogen bonds : bond 0.17915 / 12.02 ( 600) hydrogen bonds : angle 7.56587 / 5.34 ( 1440) metal coordination : bond 0.42411 / 24.83 ( 12) link_BETA1-4 : bond 0.00509 / 0.28 ( 20) link_BETA1-4 : angle 1.26893 / 0.70 ( 60) link_BETA1-6 : bond 0.00106 / 0.05 ( 4) link_BETA1-6 : angle 0.79297 / 0.53 ( 12) link_NAG-ASN : bond 0.01600 / 0.98 ( 18) link_NAG-ASN : angle 5.49899 / 3.65 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 564 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 LYS cc_start: 0.8246 (ptmm) cc_final: 0.7864 (pttp) REVERT: B 299 GLU cc_start: 0.6447 (mp0) cc_final: 0.6071 (mp0) REVERT: B 315 MET cc_start: 0.8558 (mmm) cc_final: 0.8351 (mmm) REVERT: B 578 ARG cc_start: 0.7822 (mtt90) cc_final: 0.7566 (mtt180) REVERT: A 286 ASP cc_start: 0.6452 (t70) cc_final: 0.6163 (t0) REVERT: A 350 MET cc_start: 0.8607 (mtp) cc_final: 0.8362 (mtt) REVERT: C 217 PHE cc_start: 0.8436 (m-80) cc_final: 0.8150 (m-80) REVERT: C 251 GLU cc_start: 0.7011 (tt0) cc_final: 0.6687 (tt0) REVERT: C 279 MET cc_start: 0.4682 (mtt) cc_final: 0.4290 (mtt) REVERT: C 313 TYR cc_start: 0.7899 (m-80) cc_final: 0.7514 (m-80) REVERT: C 350 MET cc_start: 0.8794 (mtp) cc_final: 0.8575 (mtm) REVERT: C 370 ASN cc_start: 0.7507 (t0) cc_final: 0.7157 (t0) REVERT: C 422 ASP cc_start: 0.7992 (t0) cc_final: 0.7016 (m-30) REVERT: C 561 ARG cc_start: 0.7971 (mtt-85) cc_final: 0.7738 (mtt180) REVERT: D 113 TYR cc_start: 0.8169 (t80) cc_final: 0.7868 (t80) REVERT: D 215 GLN cc_start: 0.7717 (pt0) cc_final: 0.6772 (pt0) REVERT: D 227 THR cc_start: 0.8207 (m) cc_final: 0.7951 (p) REVERT: D 313 TYR cc_start: 0.7851 (m-80) cc_final: 0.7416 (m-80) REVERT: D 422 ASP cc_start: 0.8450 (t0) cc_final: 0.7429 (m-30) REVERT: D 489 CYS cc_start: 0.7588 (m) cc_final: 0.7383 (m) REVERT: D 502 GLU cc_start: 0.6554 (tt0) cc_final: 0.6344 (tt0) REVERT: D 578 ARG cc_start: 0.7921 (ttm170) cc_final: 0.7586 (mtm-85) REVERT: D 579 ARG cc_start: 0.7415 (mtp85) cc_final: 0.6896 (mtt-85) outliers start: 3 outliers final: 0 residues processed: 565 average time/residue: 0.6105 time to fit residues: 384.5571 Evaluate side-chains 469 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 ASN B 72 ASN B 145 GLN B 215 GLN B 307 GLN B 341 GLN B 413 GLN B 574 GLN A 66 ASN A 72 ASN A 145 GLN A 296 GLN A 447 ASN C 72 ASN C 189 HIS C 341 GLN C 513 GLN C 554 HIS D 72 ASN D 341 GLN D 513 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.137921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119159 restraints weight = 22580.242| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.72 r_work: 0.3457 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18376 Z= 0.158 Angle : 0.664 8.964 25003 Z= 0.352 Chirality : 0.046 0.169 2753 Planarity : 0.004 0.032 3174 Dihedral : 6.536 35.884 2428 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.06 % Allowed : 10.82 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2117 helix: -0.23 (0.30), residues: 266 sheet: 0.41 (0.21), residues: 541 loop : 0.01 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 74 TYR 0.020 0.001 TYR D 97 PHE 0.023 0.002 PHE C 245 TRP 0.017 0.002 TRP B 361 HIS 0.009 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (18301) covalent geometry : angle 0.64892 / 0.35 (24835) SS BOND : bond 0.00473 / 0.29 ( 21) SS BOND : angle 1.81677 / 1.30 ( 42) hydrogen bonds : bond 0.04894 / 3.15 ( 600) hydrogen bonds : angle 6.13554 / 4.30 ( 1440) metal coordination : bond 0.02181 / 1.24 ( 12) link_BETA1-4 : bond 0.00408 / 0.25 ( 20) link_BETA1-4 : angle 1.40130 / 0.99 ( 60) link_BETA1-6 : bond 0.00323 / 0.16 ( 4) link_BETA1-6 : angle 1.45016 / 0.99 ( 12) link_NAG-ASN : bond 0.00298 / 0.14 ( 18) link_NAG-ASN : angle 2.23499 / 1.78 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 476 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7965 (p0) REVERT: B 107 CYS cc_start: 0.7175 (p) cc_final: 0.6967 (p) REVERT: A 66 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7929 (p0) REVERT: A 251 GLU cc_start: 0.7999 (tt0) cc_final: 0.7780 (tt0) REVERT: A 316 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: C 131 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7337 (mt-10) REVERT: C 154 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7681 (mt-10) REVERT: C 156 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7474 (mm-30) REVERT: C 217 PHE cc_start: 0.8672 (m-80) cc_final: 0.8321 (m-80) REVERT: C 251 GLU cc_start: 0.7934 (tt0) cc_final: 0.7625 (tt0) REVERT: C 279 MET cc_start: 0.5239 (mtt) cc_final: 0.4929 (mtp) REVERT: C 317 PHE cc_start: 0.8398 (t80) cc_final: 0.8172 (t80) REVERT: D 113 TYR cc_start: 0.8381 (t80) cc_final: 0.8077 (t80) REVERT: D 154 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7867 (mt-10) REVERT: D 207 ASP cc_start: 0.7248 (t0) cc_final: 0.7015 (t0) REVERT: D 209 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7569 (mt-10) REVERT: D 242 ARG cc_start: 0.7867 (mtt180) cc_final: 0.7558 (mtt90) outliers start: 39 outliers final: 16 residues processed: 491 average time/residue: 0.6270 time to fit residues: 341.4298 Evaluate side-chains 473 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 454 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 538 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 38 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 99 optimal weight: 0.3980 chunk 183 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 GLN B 341 GLN B 370 ASN B 558 ASN B 574 GLN A 66 ASN A 399 GLN C 182 GLN C 189 HIS C 474 ASN D 136 HIS D 215 GLN D 341 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.138249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119462 restraints weight = 22723.837| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.74 r_work: 0.3464 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18376 Z= 0.136 Angle : 0.585 8.103 25003 Z= 0.311 Chirality : 0.044 0.153 2753 Planarity : 0.003 0.031 3174 Dihedral : 5.892 39.075 2428 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.53 % Allowed : 13.72 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2117 helix: 0.25 (0.32), residues: 264 sheet: 0.24 (0.21), residues: 579 loop : 0.01 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 252 TYR 0.017 0.001 TYR D 175 PHE 0.015 0.002 PHE B 593 TRP 0.013 0.001 TRP B 361 HIS 0.007 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (18301) covalent geometry : angle 0.57278 / 0.31 (24835) SS BOND : bond 0.00245 / 0.16 ( 21) SS BOND : angle 1.77303 / 1.36 ( 42) hydrogen bonds : bond 0.04271 / 2.74 ( 600) hydrogen bonds : angle 5.75000 / 4.00 ( 1440) metal coordination : bond 0.00613 / 0.32 ( 12) link_BETA1-4 : bond 0.00394 / 0.25 ( 20) link_BETA1-4 : angle 1.22135 / 0.85 ( 60) link_BETA1-6 : bond 0.00321 / 0.16 ( 4) link_BETA1-6 : angle 1.24696 / 0.84 ( 12) link_NAG-ASN : bond 0.00165 / 0.10 ( 18) link_NAG-ASN : angle 1.78232 / 1.46 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 485 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8274 (mm-40) REVERT: B 209 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: A 66 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.8018 (p0) REVERT: A 316 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: A 472 TYR cc_start: 0.8409 (m-80) cc_final: 0.8134 (m-80) REVERT: C 154 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7591 (mt-10) REVERT: C 156 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7534 (mm-30) REVERT: C 182 GLN cc_start: 0.7752 (mt0) cc_final: 0.7503 (mt0) REVERT: C 217 PHE cc_start: 0.8640 (m-80) cc_final: 0.8388 (m-80) REVERT: C 251 GLU cc_start: 0.7951 (tt0) cc_final: 0.7741 (tt0) REVERT: C 279 MET cc_start: 0.5085 (mtt) cc_final: 0.4829 (mtp) REVERT: C 317 PHE cc_start: 0.8432 (t80) cc_final: 0.8161 (t80) REVERT: C 561 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7515 (mtt180) REVERT: D 113 TYR cc_start: 0.8392 (t80) cc_final: 0.8086 (t80) REVERT: D 123 GLN cc_start: 0.8542 (mt0) cc_final: 0.8190 (mt0) REVERT: D 154 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7858 (mt-10) REVERT: D 209 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7695 (mt-10) REVERT: D 521 MET cc_start: 0.8272 (mtp) cc_final: 0.8065 (mtm) outliers start: 48 outliers final: 19 residues processed: 501 average time/residue: 0.6119 time to fit residues: 340.4690 Evaluate side-chains 486 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 463 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 398 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 39 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 149 optimal weight: 0.0670 chunk 165 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN A 66 ASN A 399 GLN A 455 GLN C 189 HIS C 474 ASN C 554 HIS D 341 GLN D 345 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.137167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.118450 restraints weight = 22528.994| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.72 r_work: 0.3448 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18376 Z= 0.191 Angle : 0.599 7.671 25003 Z= 0.319 Chirality : 0.045 0.148 2753 Planarity : 0.004 0.052 3174 Dihedral : 5.848 42.045 2428 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.80 % Allowed : 16.04 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.18), residues: 2117 helix: 0.30 (0.32), residues: 265 sheet: 0.25 (0.21), residues: 577 loop : -0.09 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 579 TYR 0.026 0.002 TYR D 175 PHE 0.018 0.002 PHE C 527 TRP 0.015 0.002 TRP B 361 HIS 0.008 0.002 HIS B 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (18301) covalent geometry : angle 0.58481 / 0.32 (24835) SS BOND : bond 0.00298 / 0.19 ( 21) SS BOND : angle 2.06814 / 1.50 ( 42) hydrogen bonds : bond 0.04382 / 2.83 ( 600) hydrogen bonds : angle 5.72659 / 3.98 ( 1440) metal coordination : bond 0.01115 / 0.61 ( 12) link_BETA1-4 : bond 0.00388 / 0.24 ( 20) link_BETA1-4 : angle 1.22386 / 0.86 ( 60) link_BETA1-6 : bond 0.00285 / 0.14 ( 4) link_BETA1-6 : angle 1.33044 / 0.90 ( 12) link_NAG-ASN : bond 0.00208 / 0.13 ( 18) link_NAG-ASN : angle 1.78286 / 1.50 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 473 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7885 (p0) REVERT: A 316 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: C 154 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7775 (mt-10) REVERT: C 156 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7700 (mm-30) REVERT: C 217 PHE cc_start: 0.8634 (m-80) cc_final: 0.8376 (m-80) REVERT: C 251 GLU cc_start: 0.7900 (tt0) cc_final: 0.7675 (tt0) REVERT: C 455 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: C 561 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7557 (mtt180) REVERT: D 123 GLN cc_start: 0.8560 (mt0) cc_final: 0.8224 (mt0) REVERT: D 154 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7849 (mt-10) REVERT: D 237 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8290 (t) REVERT: D 521 MET cc_start: 0.8248 (mtp) cc_final: 0.8039 (mtm) outliers start: 53 outliers final: 29 residues processed: 495 average time/residue: 0.6494 time to fit residues: 357.1960 Evaluate side-chains 499 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 465 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 577 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 19 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.0030 chunk 193 optimal weight: 1.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 370 ASN A 66 ASN A 275 ASN C 177 ASN C 189 HIS C 573 HIS C 574 GLN D 341 GLN D 345 GLN D 573 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.136685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118212 restraints weight = 22526.678| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.70 r_work: 0.3444 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18376 Z= 0.187 Angle : 0.583 7.402 25003 Z= 0.311 Chirality : 0.045 0.145 2753 Planarity : 0.004 0.041 3174 Dihedral : 5.788 43.892 2428 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.27 % Allowed : 16.25 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.18), residues: 2117 helix: 0.37 (0.32), residues: 263 sheet: 0.25 (0.21), residues: 568 loop : -0.13 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 579 TYR 0.019 0.001 TYR D 175 PHE 0.017 0.002 PHE C 527 TRP 0.014 0.002 TRP B 361 HIS 0.010 0.001 HIS B 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (18301) covalent geometry : angle 0.56827 / 0.31 (24835) SS BOND : bond 0.00425 / 0.26 ( 21) SS BOND : angle 2.15998 / 1.50 ( 42) hydrogen bonds : bond 0.04231 / 2.72 ( 600) hydrogen bonds : angle 5.70148 / 3.96 ( 1440) metal coordination : bond 0.01007 / 0.56 ( 12) link_BETA1-4 : bond 0.00397 / 0.25 ( 20) link_BETA1-4 : angle 1.20477 / 0.85 ( 60) link_BETA1-6 : bond 0.00234 / 0.12 ( 4) link_BETA1-6 : angle 1.29398 / 0.88 ( 12) link_NAG-ASN : bond 0.00190 / 0.12 ( 18) link_NAG-ASN : angle 1.73772 / 1.48 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 470 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7710 (p0) REVERT: A 316 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: A 325 GLU cc_start: 0.7519 (mp0) cc_final: 0.7274 (mp0) REVERT: C 154 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7797 (mt-10) REVERT: C 156 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7703 (mm-30) REVERT: C 217 PHE cc_start: 0.8612 (m-80) cc_final: 0.8366 (m-80) REVERT: C 251 GLU cc_start: 0.7882 (tt0) cc_final: 0.7678 (tt0) REVERT: C 316 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7560 (tp40) REVERT: C 317 PHE cc_start: 0.8493 (t80) cc_final: 0.8004 (t80) REVERT: C 339 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.8078 (mtt180) REVERT: C 561 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7587 (mtt180) REVERT: D 123 GLN cc_start: 0.8557 (mt0) cc_final: 0.8212 (mt0) REVERT: D 154 GLU cc_start: 0.8555 (mt-10) cc_final: 0.7888 (mt-10) REVERT: D 209 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7745 (mt-10) outliers start: 62 outliers final: 39 residues processed: 497 average time/residue: 0.6687 time to fit residues: 369.2222 Evaluate side-chains 505 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 461 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 452 ASP Chi-restraints excluded: chain D residue 577 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 31 optimal weight: 0.2980 chunk 120 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 209 optimal weight: 0.4980 chunk 146 optimal weight: 0.6980 chunk 75 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 188 GLN B 268 HIS B 370 ASN B 392 HIS A 66 ASN A 275 ASN C 182 GLN C 189 HIS C 215 GLN C 558 ASN C 574 GLN D 341 GLN D 345 GLN D 381 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.138457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120147 restraints weight = 22530.246| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.70 r_work: 0.3478 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18376 Z= 0.104 Angle : 0.523 6.674 25003 Z= 0.281 Chirality : 0.042 0.143 2753 Planarity : 0.003 0.046 3174 Dihedral : 5.505 46.391 2428 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.17 % Allowed : 16.62 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2117 helix: 0.68 (0.33), residues: 262 sheet: 0.32 (0.22), residues: 544 loop : -0.03 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 579 TYR 0.014 0.001 TYR D 175 PHE 0.019 0.001 PHE A 245 TRP 0.012 0.001 TRP C 129 HIS 0.009 0.001 HIS B 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (18301) covalent geometry : angle 0.51173 / 0.28 (24835) SS BOND : bond 0.00258 / 0.17 ( 21) SS BOND : angle 1.71982 / 1.19 ( 42) hydrogen bonds : bond 0.03586 / 2.30 ( 600) hydrogen bonds : angle 5.45651 / 3.79 ( 1440) metal coordination : bond 0.00306 / 0.17 ( 12) link_BETA1-4 : bond 0.00403 / 0.25 ( 20) link_BETA1-4 : angle 1.12560 / 0.79 ( 60) link_BETA1-6 : bond 0.00318 / 0.16 ( 4) link_BETA1-6 : angle 1.22589 / 0.84 ( 12) link_NAG-ASN : bond 0.00108 / 0.07 ( 18) link_NAG-ASN : angle 1.53256 / 1.29 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 466 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.7553 (OUTLIER) cc_final: 0.7349 (p0) REVERT: A 287 THR cc_start: 0.8257 (t) cc_final: 0.8022 (p) REVERT: A 316 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: A 325 GLU cc_start: 0.7492 (mp0) cc_final: 0.7268 (mp0) REVERT: C 154 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7756 (mt-10) REVERT: C 156 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7707 (mm-30) REVERT: C 251 GLU cc_start: 0.7863 (tt0) cc_final: 0.7648 (tt0) REVERT: C 317 PHE cc_start: 0.8429 (t80) cc_final: 0.8179 (t80) REVERT: C 339 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8069 (mtt180) REVERT: C 561 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7474 (mtt180) REVERT: D 123 GLN cc_start: 0.8550 (mt0) cc_final: 0.8205 (mt0) REVERT: D 154 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7892 (mt-10) REVERT: D 209 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7724 (mt-10) REVERT: D 237 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8245 (t) outliers start: 60 outliers final: 30 residues processed: 491 average time/residue: 0.6529 time to fit residues: 355.3161 Evaluate side-chains 499 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 464 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 398 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 101 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 188 GLN B 370 ASN A 66 ASN C 177 ASN C 182 GLN C 189 HIS C 215 GLN C 574 GLN D 341 GLN D 345 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.135891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.117081 restraints weight = 22479.563| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.74 r_work: 0.3433 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18376 Z= 0.228 Angle : 0.602 8.902 25003 Z= 0.320 Chirality : 0.046 0.142 2753 Planarity : 0.004 0.056 3174 Dihedral : 5.747 47.321 2428 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.11 % Allowed : 17.73 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2117 helix: 0.48 (0.32), residues: 265 sheet: 0.31 (0.22), residues: 557 loop : -0.13 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 402 TYR 0.015 0.002 TYR D 403 PHE 0.021 0.002 PHE C 527 TRP 0.014 0.002 TRP B 361 HIS 0.011 0.002 HIS B 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (18301) covalent geometry : angle 0.58841 / 0.32 (24835) SS BOND : bond 0.00328 / 0.21 ( 21) SS BOND : angle 2.11679 / 1.42 ( 42) hydrogen bonds : bond 0.04382 / 2.84 ( 600) hydrogen bonds : angle 5.66156 / 3.93 ( 1440) metal coordination : bond 0.01295 / 0.74 ( 12) link_BETA1-4 : bond 0.00388 / 0.25 ( 20) link_BETA1-4 : angle 1.19754 / 0.85 ( 60) link_BETA1-6 : bond 0.00266 / 0.14 ( 4) link_BETA1-6 : angle 1.36082 / 0.92 ( 12) link_NAG-ASN : bond 0.00243 / 0.15 ( 18) link_NAG-ASN : angle 1.74655 / 1.49 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 471 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: B 340 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7967 (mmtm) REVERT: A 287 THR cc_start: 0.8276 (t) cc_final: 0.8060 (p) REVERT: A 316 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: A 325 GLU cc_start: 0.7573 (mp0) cc_final: 0.7341 (mp0) REVERT: C 154 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7789 (mt-10) REVERT: C 156 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7864 (mm-30) REVERT: C 251 GLU cc_start: 0.7933 (tt0) cc_final: 0.7705 (tt0) REVERT: C 316 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7582 (tp40) REVERT: C 331 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6836 (tt0) REVERT: C 339 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8082 (mtt180) REVERT: C 402 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7501 (mtm-85) REVERT: C 561 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7673 (mtt180) REVERT: D 123 GLN cc_start: 0.8584 (mt0) cc_final: 0.8226 (mt0) REVERT: D 154 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7884 (mt-10) REVERT: D 209 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7726 (mt-10) REVERT: D 237 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8259 (t) REVERT: D 538 ILE cc_start: 0.8513 (pt) cc_final: 0.8311 (mt) outliers start: 59 outliers final: 38 residues processed: 493 average time/residue: 0.6336 time to fit residues: 347.2838 Evaluate side-chains 511 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 465 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 345 GLN Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 577 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 179 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 188 GLN B 268 HIS B 370 ASN A 455 GLN C 177 ASN C 182 GLN C 189 HIS C 574 GLN D 341 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118013 restraints weight = 22395.757| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.73 r_work: 0.3450 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18376 Z= 0.154 Angle : 0.565 12.140 25003 Z= 0.301 Chirality : 0.044 0.145 2753 Planarity : 0.004 0.049 3174 Dihedral : 5.643 48.288 2428 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.74 % Allowed : 18.31 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.18), residues: 2117 helix: 0.58 (0.32), residues: 265 sheet: 0.31 (0.22), residues: 557 loop : -0.13 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 402 TYR 0.012 0.001 TYR D 403 PHE 0.020 0.002 PHE A 245 TRP 0.012 0.001 TRP B 361 HIS 0.011 0.001 HIS B 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (18301) covalent geometry : angle 0.55208 / 0.30 (24835) SS BOND : bond 0.00334 / 0.20 ( 21) SS BOND : angle 1.95312 / 1.30 ( 42) hydrogen bonds : bond 0.03945 / 2.55 ( 600) hydrogen bonds : angle 5.57899 / 3.87 ( 1440) metal coordination : bond 0.00743 / 0.43 ( 12) link_BETA1-4 : bond 0.00390 / 0.25 ( 20) link_BETA1-4 : angle 1.15101 / 0.82 ( 60) link_BETA1-6 : bond 0.00254 / 0.13 ( 4) link_BETA1-6 : angle 1.27424 / 0.87 ( 12) link_NAG-ASN : bond 0.00143 / 0.09 ( 18) link_NAG-ASN : angle 1.63537 / 1.40 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 465 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7943 (mmtm) REVERT: A 316 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: A 325 GLU cc_start: 0.7534 (mp0) cc_final: 0.7311 (mp0) REVERT: A 472 TYR cc_start: 0.8592 (m-80) cc_final: 0.8200 (m-80) REVERT: C 154 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7858 (mt-10) REVERT: C 156 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7835 (mm-30) REVERT: C 251 GLU cc_start: 0.7901 (tt0) cc_final: 0.7673 (tt0) REVERT: C 316 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7656 (tp40) REVERT: C 317 PHE cc_start: 0.8447 (t80) cc_final: 0.7996 (t80) REVERT: C 339 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8060 (mtt180) REVERT: C 561 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7552 (mtt180) REVERT: D 123 GLN cc_start: 0.8567 (mt0) cc_final: 0.8202 (mt0) REVERT: D 154 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7881 (mt-10) REVERT: D 209 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7702 (mt-10) REVERT: D 237 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8220 (t) outliers start: 52 outliers final: 35 residues processed: 486 average time/residue: 0.6112 time to fit residues: 329.5915 Evaluate side-chains 501 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 460 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 577 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 21 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 89 optimal weight: 0.0980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 370 ASN A 455 GLN C 177 ASN C 182 GLN C 189 HIS C 574 GLN D 341 GLN D 345 GLN D 381 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.137519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.118969 restraints weight = 22335.392| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.72 r_work: 0.3459 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18376 Z= 0.128 Angle : 0.544 12.634 25003 Z= 0.289 Chirality : 0.043 0.139 2753 Planarity : 0.003 0.048 3174 Dihedral : 5.528 48.903 2428 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.69 % Allowed : 18.26 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 2117 helix: 0.79 (0.32), residues: 263 sheet: 0.24 (0.21), residues: 568 loop : -0.08 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 579 TYR 0.011 0.001 TYR A 313 PHE 0.019 0.001 PHE A 245 TRP 0.009 0.001 TRP B 361 HIS 0.011 0.001 HIS B 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (18301) covalent geometry : angle 0.53173 / 0.29 (24835) SS BOND : bond 0.00369 / 0.24 ( 21) SS BOND : angle 1.95930 / 1.26 ( 42) hydrogen bonds : bond 0.03668 / 2.36 ( 600) hydrogen bonds : angle 5.43608 / 3.78 ( 1440) metal coordination : bond 0.00561 / 0.33 ( 12) link_BETA1-4 : bond 0.00384 / 0.24 ( 20) link_BETA1-4 : angle 1.12384 / 0.79 ( 60) link_BETA1-6 : bond 0.00269 / 0.14 ( 4) link_BETA1-6 : angle 1.22673 / 0.84 ( 12) link_NAG-ASN : bond 0.00137 / 0.10 ( 18) link_NAG-ASN : angle 1.58628 / 1.31 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 463 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7906 (mmtm) REVERT: A 316 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: A 325 GLU cc_start: 0.7488 (mp0) cc_final: 0.7272 (mp0) REVERT: A 472 TYR cc_start: 0.8560 (m-80) cc_final: 0.8147 (m-80) REVERT: C 251 GLU cc_start: 0.7877 (tt0) cc_final: 0.7653 (tt0) REVERT: C 316 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7649 (tp40) REVERT: C 317 PHE cc_start: 0.8457 (t80) cc_final: 0.7935 (t80) REVERT: C 381 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: C 561 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7517 (mtt180) REVERT: D 123 GLN cc_start: 0.8565 (mt0) cc_final: 0.8205 (mt0) REVERT: D 154 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7888 (mt-10) REVERT: D 209 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7674 (mt-10) REVERT: D 237 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8203 (t) outliers start: 51 outliers final: 33 residues processed: 483 average time/residue: 0.6436 time to fit residues: 345.4325 Evaluate side-chains 490 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 451 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 577 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 10 optimal weight: 0.3980 chunk 121 optimal weight: 0.9990 chunk 169 optimal weight: 0.3980 chunk 103 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 102 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 370 ASN A 455 GLN C 177 ASN C 182 GLN C 189 HIS D 341 GLN D 345 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.138185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.119638 restraints weight = 22487.849| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.73 r_work: 0.3481 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18376 Z= 0.112 Angle : 0.533 12.834 25003 Z= 0.284 Chirality : 0.042 0.139 2753 Planarity : 0.003 0.048 3174 Dihedral : 5.475 49.044 2428 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.01 % Allowed : 19.31 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.18), residues: 2117 helix: 0.91 (0.33), residues: 263 sheet: 0.25 (0.22), residues: 575 loop : -0.05 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 579 TYR 0.009 0.001 TYR D 403 PHE 0.026 0.001 PHE A 245 TRP 0.017 0.001 TRP C 129 HIS 0.012 0.001 HIS B 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (18301) covalent geometry : angle 0.52132 / 0.28 (24835) SS BOND : bond 0.00231 / 0.13 ( 21) SS BOND : angle 1.81502 / 1.14 ( 42) hydrogen bonds : bond 0.03498 / 2.26 ( 600) hydrogen bonds : angle 5.36540 / 3.72 ( 1440) metal coordination : bond 0.00375 / 0.22 ( 12) link_BETA1-4 : bond 0.00394 / 0.24 ( 20) link_BETA1-4 : angle 1.12051 / 0.79 ( 60) link_BETA1-6 : bond 0.00312 / 0.16 ( 4) link_BETA1-6 : angle 1.20311 / 0.83 ( 12) link_NAG-ASN : bond 0.00126 / 0.09 ( 18) link_NAG-ASN : angle 1.56874 / 1.28 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 466 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 GLU cc_start: 0.7504 (mp0) cc_final: 0.7286 (mp0) REVERT: A 472 TYR cc_start: 0.8542 (m-80) cc_final: 0.8241 (m-80) REVERT: A 525 MET cc_start: 0.8324 (mmm) cc_final: 0.8083 (mmm) REVERT: C 251 GLU cc_start: 0.7847 (tt0) cc_final: 0.7623 (tt0) REVERT: C 381 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7786 (mt0) REVERT: D 123 GLN cc_start: 0.8555 (mt0) cc_final: 0.8194 (mt0) REVERT: D 154 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7816 (mt-10) REVERT: D 209 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7653 (mt-10) REVERT: D 237 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8228 (t) outliers start: 38 outliers final: 29 residues processed: 481 average time/residue: 0.6687 time to fit residues: 356.8480 Evaluate side-chains 487 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 456 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 538 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 0.0270 chunk 204 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 370 ASN C 177 ASN C 182 GLN C 189 HIS D 341 GLN D 345 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.137742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.119199 restraints weight = 22680.834| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.73 r_work: 0.3466 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18376 Z= 0.130 Angle : 0.554 13.015 25003 Z= 0.295 Chirality : 0.043 0.138 2753 Planarity : 0.004 0.057 3174 Dihedral : 5.540 49.349 2428 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.27 % Allowed : 19.53 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2117 helix: 0.89 (0.32), residues: 263 sheet: 0.27 (0.22), residues: 573 loop : -0.07 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 402 TYR 0.019 0.001 TYR D 97 PHE 0.021 0.001 PHE C 245 TRP 0.010 0.001 TRP B 567 HIS 0.013 0.001 HIS B 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (18301) covalent geometry : angle 0.54155 / 0.29 (24835) SS BOND : bond 0.00266 / 0.16 ( 21) SS BOND : angle 2.08651 / 1.27 ( 42) hydrogen bonds : bond 0.03604 / 2.32 ( 600) hydrogen bonds : angle 5.36500 / 3.73 ( 1440) metal coordination : bond 0.00531 / 0.30 ( 12) link_BETA1-4 : bond 0.00401 / 0.25 ( 20) link_BETA1-4 : angle 1.11202 / 0.79 ( 60) link_BETA1-6 : bond 0.00268 / 0.13 ( 4) link_BETA1-6 : angle 1.23363 / 0.85 ( 12) link_NAG-ASN : bond 0.00103 / 0.07 ( 18) link_NAG-ASN : angle 1.52232 / 1.26 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9191.27 seconds wall clock time: 156 minutes 34.71 seconds (9394.71 seconds total)