Starting phenix.real_space_refine on Thu Mar 5 01:20:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uaf_26423/03_2026/7uaf_26423.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uaf_26423/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uaf_26423/03_2026/7uaf_26423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uaf_26423/03_2026/7uaf_26423.map" model { file = "/net/cci-nas-00/data/ceres_data/7uaf_26423/03_2026/7uaf_26423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uaf_26423/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.24, per 1000 atoms: 0.24 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: 1.76 Conformation dependent library (CDL) restraints added in 739.5 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: 0.77 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: 3.31 Time building geometry restraints manager: 2.25 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 - 21.54: 10706 21.54 - 43.08: 497 43.08 - 64.63: 84 64.63 - 86.17: 47 86.17 - 107.71: 20 Dihedral angle restraints: 11354 sinusoidal: 5162 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 11351 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: 0.650 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.280 Find NCS groups from input model: 0.490 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:7.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 14.566 107.709 7315 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 covalent geometry : bond 0.01195 (18301) covalent geometry : angle 1.79964 (24835) SS BOND : bond 0.01858 ( 21) SS BOND : angle 2.32265 ( 42) hydrogen bonds : bond 0.17915 ( 600) hydrogen bonds : angle 7.56587 ( 1440) metal coordination : bond 0.42411 ( 12) link_BETA1-4 : bond 0.00509 ( 20) link_BETA1-4 : angle 1.26893 ( 60) link_BETA1-6 : bond 0.00106 ( 4) link_BETA1-6 : angle 0.79297 ( 12) link_NAG-ASN : bond 0.01600 ( 18) link_NAG-ASN : angle 5.49899 ( 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 : 0.587 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: 0.7865 (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: 0.4291 (mtt) REVERT: C 313 TYR cc_start: 0.7899 (m-80) cc_final: 0.7537 (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: 0.7018 (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: 0.7415 (m-80) REVERT: D 422 ASP cc_start: 0.8450 (t0) cc_final: 0.7415 (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: 0.6396 time to fit residues: 400.7976 Evaluate side-chains 468 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3838 r_free = 0.3838 target = 0.137973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.119169 restraints weight = 22591.311| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.72 r_work: 0.3457 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18376 Z= 0.157 Angle : 0.663 8.877 25003 Z= 0.352 Chirality : 0.047 0.171 2753 Planarity : 0.004 0.032 3174 Dihedral : 9.058 67.931 3286 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.11 % Allowed : 10.71 % Favored : 87.18 % 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: 0.06 (0.17), residues: 2117 helix: -0.24 (0.30), residues: 266 sheet: 0.41 (0.21), residues: 541 loop : 0.04 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 74 TYR 0.020 0.002 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 A 155 Details of bonding type rmsd covalent geometry : bond 0.00345 (18301) covalent geometry : angle 0.64721 (24835) SS BOND : bond 0.00528 ( 21) SS BOND : angle 1.91117 ( 42) hydrogen bonds : bond 0.04973 ( 600) hydrogen bonds : angle 6.12807 ( 1440) metal coordination : bond 0.01771 ( 12) link_BETA1-4 : bond 0.00471 ( 20) link_BETA1-4 : angle 1.73302 ( 60) link_BETA1-6 : bond 0.00335 ( 4) link_BETA1-6 : angle 1.41326 ( 12) link_NAG-ASN : bond 0.00320 ( 18) link_NAG-ASN : angle 2.13168 ( 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 514 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 474 time to evaluate : 0.606 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: 0.7948 (p0) REVERT: A 66 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7921 (p0) REVERT: A 316 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: C 154 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7692 (mt-10) REVERT: C 156 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7470 (mm-30) REVERT: C 217 PHE cc_start: 0.8668 (m-80) cc_final: 0.8322 (m-80) REVERT: C 251 GLU cc_start: 0.7915 (tt0) cc_final: 0.7611 (tt0) REVERT: C 279 MET cc_start: 0.5258 (mtt) cc_final: 0.4953 (mtp) REVERT: C 317 PHE cc_start: 0.8399 (t80) cc_final: 0.8160 (t80) REVERT: D 113 TYR cc_start: 0.8382 (t80) cc_final: 0.8070 (t80) REVERT: D 154 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7855 (mt-10) REVERT: D 207 ASP cc_start: 0.7281 (t0) cc_final: 0.7058 (t0) REVERT: D 209 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7537 (mt-10) REVERT: D 242 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7546 (mtt90) outliers start: 40 outliers final: 17 residues processed: 489 average time/residue: 0.6690 time to fit residues: 361.9082 Evaluate side-chains 473 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 453 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 577 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 38 optimal weight: 0.0030 chunk 92 optimal weight: 0.8980 chunk 137 optimal weight: 0.0270 chunk 187 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 99 optimal weight: 0.0970 chunk 183 optimal weight: 1.9990 chunk 160 optimal weight: 0.3980 chunk 117 optimal weight: 0.0870 overall best weight: 0.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 292 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 341 GLN D 487 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.140242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121678 restraints weight = 22851.991| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.74 r_work: 0.3502 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18376 Z= 0.113 Angle : 0.563 7.556 25003 Z= 0.298 Chirality : 0.043 0.145 2753 Planarity : 0.003 0.031 3174 Dihedral : 6.755 45.959 3286 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.06 % Allowed : 13.98 % Favored : 83.96 % 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: 0.25 (0.18), residues: 2117 helix: 0.62 (0.33), residues: 256 sheet: 0.31 (0.21), residues: 572 loop : 0.10 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 252 TYR 0.016 0.001 TYR D 175 PHE 0.013 0.001 PHE C 245 TRP 0.013 0.001 TRP C 129 HIS 0.007 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00212 (18301) covalent geometry : angle 0.54895 (24835) SS BOND : bond 0.00632 ( 21) SS BOND : angle 1.76360 ( 42) hydrogen bonds : bond 0.03812 ( 600) hydrogen bonds : angle 5.57992 ( 1440) metal coordination : bond 0.00246 ( 12) link_BETA1-4 : bond 0.00397 ( 20) link_BETA1-4 : angle 1.62841 ( 60) link_BETA1-6 : bond 0.00351 ( 4) link_BETA1-6 : angle 1.17618 ( 12) link_NAG-ASN : bond 0.00277 ( 18) link_NAG-ASN : angle 1.62104 ( 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 522 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 483 time to evaluate : 0.671 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 107 CYS cc_start: 0.7224 (p) cc_final: 0.7017 (p) REVERT: B 209 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: A 472 TYR cc_start: 0.8298 (m-80) cc_final: 0.7982 (m-80) REVERT: C 154 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7504 (mt-10) REVERT: C 156 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7499 (mm-30) REVERT: C 182 GLN cc_start: 0.7690 (mt0) cc_final: 0.7480 (mt0) REVERT: C 217 PHE cc_start: 0.8652 (m-80) cc_final: 0.8321 (m-80) REVERT: C 251 GLU cc_start: 0.7942 (tt0) cc_final: 0.7727 (tt0) REVERT: C 279 MET cc_start: 0.5147 (mtt) cc_final: 0.4889 (mtp) REVERT: C 315 MET cc_start: 0.8486 (mmt) cc_final: 0.8004 (mmt) REVERT: C 317 PHE cc_start: 0.8388 (t80) cc_final: 0.8161 (t80) REVERT: D 113 TYR cc_start: 0.8357 (t80) cc_final: 0.8067 (t80) REVERT: D 123 GLN cc_start: 0.8528 (mt0) cc_final: 0.8188 (mt0) REVERT: D 154 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7759 (mt-10) REVERT: D 209 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7668 (mt-10) REVERT: D 579 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7453 (mtt-85) outliers start: 39 outliers final: 18 residues processed: 497 average time/residue: 0.6851 time to fit residues: 376.5983 Evaluate side-chains 482 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 463 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 377 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain C residue 107 CYS 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 39 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 191 optimal weight: 0.5980 chunk 171 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 chunk 165 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 187 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 145 GLN B 188 GLN B 370 ASN B 392 HIS A 66 ASN A 399 GLN C 189 HIS C 474 ASN C 554 HIS D 341 GLN D 345 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.138988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.120371 restraints weight = 22642.095| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.73 r_work: 0.3485 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2737 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= 0.117 Angle : 0.543 8.300 25003 Z= 0.288 Chirality : 0.043 0.149 2753 Planarity : 0.003 0.054 3174 Dihedral : 5.617 44.148 3286 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.69 % Allowed : 15.62 % Favored : 81.69 % 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: 0.26 (0.18), residues: 2117 helix: 0.66 (0.33), residues: 263 sheet: 0.32 (0.21), residues: 581 loop : 0.10 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 402 TYR 0.022 0.001 TYR D 175 PHE 0.015 0.001 PHE C 527 TRP 0.011 0.001 TRP C 129 HIS 0.007 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00260 (18301) covalent geometry : angle 0.52819 (24835) SS BOND : bond 0.00358 ( 21) SS BOND : angle 1.80043 ( 42) hydrogen bonds : bond 0.03741 ( 600) hydrogen bonds : angle 5.41060 ( 1440) metal coordination : bond 0.00513 ( 12) link_BETA1-4 : bond 0.00402 ( 20) link_BETA1-4 : angle 1.56618 ( 60) link_BETA1-6 : bond 0.00288 ( 4) link_BETA1-6 : angle 1.23888 ( 12) link_NAG-ASN : bond 0.00142 ( 18) link_NAG-ASN : angle 1.59626 ( 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 523 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 472 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 594 GLU cc_start: 0.7547 (pm20) cc_final: 0.7308 (pm20) REVERT: A 66 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8012 (p0) REVERT: A 275 ASN cc_start: 0.8179 (p0) cc_final: 0.7933 (p0) REVERT: A 472 TYR cc_start: 0.8335 (m-80) cc_final: 0.8015 (m-80) REVERT: C 154 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7641 (mt-10) REVERT: C 156 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7781 (mm-30) REVERT: C 217 PHE cc_start: 0.8621 (m-80) cc_final: 0.8293 (m-80) REVERT: C 251 GLU cc_start: 0.7881 (tt0) cc_final: 0.7666 (tt0) REVERT: C 279 MET cc_start: 0.4947 (mtt) cc_final: 0.4724 (mtp) REVERT: C 317 PHE cc_start: 0.8450 (t80) cc_final: 0.8204 (t80) REVERT: C 561 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7311 (mtt180) REVERT: D 74 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.5536 (mpt180) REVERT: D 113 TYR cc_start: 0.8348 (t80) cc_final: 0.8054 (t80) REVERT: D 123 GLN cc_start: 0.8554 (mt0) cc_final: 0.8216 (mt0) REVERT: D 154 GLU cc_start: 0.8502 (mt-10) cc_final: 0.7868 (mt-10) REVERT: D 207 ASP cc_start: 0.7222 (t0) cc_final: 0.6923 (t0) REVERT: D 209 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7417 (mt-10) outliers start: 51 outliers final: 27 residues processed: 490 average time/residue: 0.6576 time to fit residues: 357.2860 Evaluate side-chains 487 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 457 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 288 ASP 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 A residue 66 ASN 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 425 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 489 CYS 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 178 ILE Chi-restraints excluded: chain C residue 228 ILE 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 74 ARG Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 251 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 19 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 GLN B 370 ASN A 189 HIS C 177 ASN C 182 GLN C 189 HIS D 136 HIS 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 = 0.137818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.119080 restraints weight = 22435.092| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.73 r_work: 0.3454 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18376 Z= 0.165 Angle : 0.567 7.277 25003 Z= 0.302 Chirality : 0.044 0.147 2753 Planarity : 0.004 0.052 3174 Dihedral : 5.408 44.770 3286 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.01 % Allowed : 16.57 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.61 (0.33), residues: 263 sheet: 0.31 (0.21), residues: 594 loop : -0.01 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 579 TYR 0.017 0.001 TYR D 175 PHE 0.018 0.002 PHE C 527 TRP 0.012 0.001 TRP B 361 HIS 0.009 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00386 (18301) covalent geometry : angle 0.55133 (24835) SS BOND : bond 0.00309 ( 21) SS BOND : angle 2.22642 ( 42) hydrogen bonds : bond 0.04053 ( 600) hydrogen bonds : angle 5.52359 ( 1440) metal coordination : bond 0.00780 ( 12) link_BETA1-4 : bond 0.00408 ( 20) link_BETA1-4 : angle 1.43389 ( 60) link_BETA1-6 : bond 0.00235 ( 4) link_BETA1-6 : angle 1.28128 ( 12) link_NAG-ASN : bond 0.00174 ( 18) link_NAG-ASN : angle 1.67152 ( 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 527 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 470 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 GLU cc_start: 0.7507 (mp0) cc_final: 0.7275 (mp0) REVERT: C 217 PHE cc_start: 0.8621 (m-80) cc_final: 0.8383 (m-80) REVERT: C 251 GLU cc_start: 0.7926 (tt0) cc_final: 0.7705 (tt0) REVERT: C 272 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: C 316 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7566 (tp40) REVERT: C 317 PHE cc_start: 0.8494 (t80) cc_final: 0.7965 (t80) REVERT: C 561 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7520 (mtt180) REVERT: D 123 GLN cc_start: 0.8560 (mt0) cc_final: 0.8210 (mt0) REVERT: D 154 GLU cc_start: 0.8514 (mt-10) cc_final: 0.7844 (mt-10) REVERT: D 207 ASP cc_start: 0.7266 (t0) cc_final: 0.6986 (t0) REVERT: D 525 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8253 (mmm) outliers start: 57 outliers final: 31 residues processed: 492 average time/residue: 0.6239 time to fit residues: 339.9150 Evaluate side-chains 498 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 463 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 288 ASP 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 237 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 308 CYS 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 C residue 107 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 402 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 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 345 GLN Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 452 ASP Chi-restraints excluded: chain D residue 525 MET 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: 0.9990 chunk 120 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 117 optimal weight: 0.4980 chunk 147 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 209 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN B 188 GLN B 268 HIS B 370 ASN A 189 HIS A 275 ASN C 177 ASN C 182 GLN C 189 HIS C 574 GLN D 341 GLN D 345 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.138745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.120099 restraints weight = 22422.838| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.73 r_work: 0.3471 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18376 Z= 0.126 Angle : 0.542 9.032 25003 Z= 0.288 Chirality : 0.043 0.148 2753 Planarity : 0.003 0.048 3174 Dihedral : 5.243 45.887 3286 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.90 % Allowed : 17.52 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.19 (0.18), residues: 2117 helix: 0.67 (0.33), residues: 265 sheet: 0.33 (0.22), residues: 570 loop : 0.00 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 579 TYR 0.014 0.001 TYR B 187 PHE 0.018 0.001 PHE A 245 TRP 0.012 0.001 TRP C 129 HIS 0.010 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00289 (18301) covalent geometry : angle 0.52609 (24835) SS BOND : bond 0.00462 ( 21) SS BOND : angle 2.27273 ( 42) hydrogen bonds : bond 0.03671 ( 600) hydrogen bonds : angle 5.43525 ( 1440) metal coordination : bond 0.00512 ( 12) link_BETA1-4 : bond 0.00415 ( 20) link_BETA1-4 : angle 1.32553 ( 60) link_BETA1-6 : bond 0.00256 ( 4) link_BETA1-6 : angle 1.23923 ( 12) link_NAG-ASN : bond 0.00151 ( 18) link_NAG-ASN : angle 1.59312 ( 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 522 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 467 time to evaluate : 0.591 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 188 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7765 (mp10) REVERT: A 325 GLU cc_start: 0.7494 (mp0) cc_final: 0.7260 (mp0) REVERT: C 101 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7576 (mpp) REVERT: C 217 PHE cc_start: 0.8604 (m-80) cc_final: 0.8255 (m-80) REVERT: C 251 GLU cc_start: 0.7934 (tt0) cc_final: 0.7720 (tt0) REVERT: C 317 PHE cc_start: 0.8480 (t80) cc_final: 0.8205 (t80) REVERT: C 355 SER cc_start: 0.7995 (m) cc_final: 0.7721 (t) REVERT: C 561 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7454 (mtt180) REVERT: D 123 GLN cc_start: 0.8565 (mt0) cc_final: 0.8208 (mt0) REVERT: D 154 GLU cc_start: 0.8491 (mt-10) cc_final: 0.7886 (mt-10) REVERT: D 207 ASP cc_start: 0.7247 (t0) cc_final: 0.6975 (t0) REVERT: D 209 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7476 (mt-10) REVERT: D 272 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.5258 (mm-30) outliers start: 55 outliers final: 31 residues processed: 489 average time/residue: 0.6625 time to fit residues: 358.7006 Evaluate side-chains 500 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 465 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 288 ASP 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 237 SER Chi-restraints excluded: chain A residue 308 CYS 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 A residue 592 ASP Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 318 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 101 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 0.0010 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 145 GLN B 188 GLN B 268 HIS B 370 ASN A 189 HIS A 275 ASN C 66 ASN C 177 ASN C 182 GLN C 189 HIS C 574 GLN D 341 GLN D 345 GLN D 381 GLN D 573 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.137572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.119150 restraints weight = 22573.680| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.72 r_work: 0.3456 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18376 Z= 0.164 Angle : 0.567 10.437 25003 Z= 0.301 Chirality : 0.044 0.153 2753 Planarity : 0.004 0.049 3174 Dihedral : 5.242 47.844 3286 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.80 % Allowed : 17.57 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.14 (0.18), residues: 2117 helix: 0.63 (0.32), residues: 265 sheet: 0.34 (0.22), residues: 569 loop : -0.05 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 402 TYR 0.015 0.001 TYR B 187 PHE 0.022 0.002 PHE A 245 TRP 0.011 0.001 TRP B 361 HIS 0.011 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00384 (18301) covalent geometry : angle 0.55135 (24835) SS BOND : bond 0.00357 ( 21) SS BOND : angle 2.32070 ( 42) hydrogen bonds : bond 0.03901 ( 600) hydrogen bonds : angle 5.49126 ( 1440) metal coordination : bond 0.00814 ( 12) link_BETA1-4 : bond 0.00415 ( 20) link_BETA1-4 : angle 1.30982 ( 60) link_BETA1-6 : bond 0.00219 ( 4) link_BETA1-6 : angle 1.29252 ( 12) link_NAG-ASN : bond 0.00160 ( 18) link_NAG-ASN : angle 1.66282 ( 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 514 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 461 time to evaluate : 0.698 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 325 GLU cc_start: 0.7529 (mp0) cc_final: 0.7313 (mp0) REVERT: C 251 GLU cc_start: 0.7914 (tt0) cc_final: 0.7681 (tt0) REVERT: C 316 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7546 (tp40) REVERT: C 317 PHE cc_start: 0.8492 (t80) cc_final: 0.7949 (t80) REVERT: C 561 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7535 (mtt180) REVERT: D 123 GLN cc_start: 0.8577 (mt0) cc_final: 0.8223 (mt0) REVERT: D 154 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7901 (mt-10) REVERT: D 207 ASP cc_start: 0.7286 (t0) cc_final: 0.7016 (t0) REVERT: D 209 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7480 (mt-10) REVERT: D 538 ILE cc_start: 0.8516 (pt) cc_final: 0.8311 (mt) outliers start: 53 outliers final: 33 residues processed: 481 average time/residue: 0.6583 time to fit residues: 349.5004 Evaluate side-chains 490 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 455 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 288 ASP 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 A residue 237 SER Chi-restraints excluded: chain A residue 308 CYS 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 A residue 592 ASP Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 318 SER 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 591 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 179 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 370 ASN A 189 HIS C 66 ASN C 177 ASN C 182 GLN C 189 HIS C 574 GLN D 341 GLN D 345 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.137591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.118952 restraints weight = 22375.173| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.73 r_work: 0.3456 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18376 Z= 0.158 Angle : 0.567 11.291 25003 Z= 0.300 Chirality : 0.044 0.160 2753 Planarity : 0.004 0.048 3174 Dihedral : 5.230 49.337 3286 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.53 % Allowed : 17.94 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.10 (0.18), residues: 2117 helix: 0.69 (0.32), residues: 263 sheet: 0.32 (0.22), residues: 562 loop : -0.11 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 402 TYR 0.012 0.001 TYR D 403 PHE 0.021 0.002 PHE B 593 TRP 0.011 0.001 TRP B 361 HIS 0.011 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00372 (18301) covalent geometry : angle 0.55145 (24835) SS BOND : bond 0.00339 ( 21) SS BOND : angle 2.35377 ( 42) hydrogen bonds : bond 0.03854 ( 600) hydrogen bonds : angle 5.50973 ( 1440) metal coordination : bond 0.00774 ( 12) link_BETA1-4 : bond 0.00427 ( 20) link_BETA1-4 : angle 1.26300 ( 60) link_BETA1-6 : bond 0.00215 ( 4) link_BETA1-6 : angle 1.29351 ( 12) link_NAG-ASN : bond 0.00145 ( 18) link_NAG-ASN : angle 1.65426 ( 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 511 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 463 time to evaluate : 0.462 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: 0.7555 (mp0) cc_final: 0.7339 (mp0) REVERT: C 251 GLU cc_start: 0.7922 (tt0) cc_final: 0.7690 (tt0) REVERT: C 316 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7701 (tp40) REVERT: C 317 PHE cc_start: 0.8468 (t80) cc_final: 0.7952 (t80) REVERT: C 411 ASP cc_start: 0.7495 (t0) cc_final: 0.7284 (t0) REVERT: C 561 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7532 (mtt180) REVERT: D 123 GLN cc_start: 0.8572 (mt0) cc_final: 0.8211 (mt0) REVERT: D 154 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7864 (mt-10) REVERT: D 209 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7702 (mt-10) outliers start: 48 outliers final: 34 residues processed: 483 average time/residue: 0.6252 time to fit residues: 334.0301 Evaluate side-chains 493 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 457 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 288 ASP 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 557 CYS Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 261 THR 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 249 ASP Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 318 SER 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 591 VAL Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 288 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: 0.7980 chunk 105 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 370 ASN A 189 HIS A 455 GLN C 177 ASN C 182 GLN C 189 HIS C 574 GLN D 341 GLN D 345 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.138113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119579 restraints weight = 22230.773| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.72 r_work: 0.3468 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18376 Z= 0.136 Angle : 0.561 12.761 25003 Z= 0.297 Chirality : 0.043 0.158 2753 Planarity : 0.003 0.048 3174 Dihedral : 5.215 49.930 3286 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.48 % Allowed : 18.15 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.13 (0.18), residues: 2117 helix: 0.75 (0.32), residues: 263 sheet: 0.24 (0.22), residues: 567 loop : -0.05 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 402 TYR 0.011 0.001 TYR D 403 PHE 0.019 0.001 PHE C 245 TRP 0.009 0.001 TRP C 129 HIS 0.012 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00317 (18301) covalent geometry : angle 0.54418 (24835) SS BOND : bond 0.00332 ( 21) SS BOND : angle 2.51873 ( 42) hydrogen bonds : bond 0.03662 ( 600) hydrogen bonds : angle 5.45015 ( 1440) metal coordination : bond 0.00586 ( 12) link_BETA1-4 : bond 0.00411 ( 20) link_BETA1-4 : angle 1.22284 ( 60) link_BETA1-6 : bond 0.00225 ( 4) link_BETA1-6 : angle 1.26183 ( 12) link_NAG-ASN : bond 0.00126 ( 18) link_NAG-ASN : angle 1.59402 ( 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 511 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 464 time to evaluate : 0.425 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 313 TYR cc_start: 0.8631 (m-80) cc_final: 0.8409 (m-80) REVERT: A 325 GLU cc_start: 0.7513 (mp0) cc_final: 0.7303 (mp0) REVERT: C 251 GLU cc_start: 0.7880 (tt0) cc_final: 0.7661 (tt0) REVERT: C 411 ASP cc_start: 0.7466 (t0) cc_final: 0.7214 (t0) REVERT: D 123 GLN cc_start: 0.8558 (mt0) cc_final: 0.8198 (mt0) REVERT: D 154 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7873 (mt-10) REVERT: D 209 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7660 (mt-10) outliers start: 47 outliers final: 37 residues processed: 480 average time/residue: 0.6854 time to fit residues: 362.5062 Evaluate side-chains 494 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 457 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 288 ASP 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 557 CYS Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 261 THR 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 249 ASP Chi-restraints excluded: chain C residue 318 SER 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 575 MET Chi-restraints excluded: chain C residue 591 VAL 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 288 ASP 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: 0.6980 chunk 121 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 182 optimal weight: 0.0070 chunk 79 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 370 ASN A 189 HIS C 177 ASN C 182 GLN C 189 HIS C 215 GLN C 574 GLN D 177 ASN D 341 GLN D 345 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.138553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120057 restraints weight = 22354.213| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.73 r_work: 0.3473 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18376 Z= 0.124 Angle : 0.558 13.253 25003 Z= 0.295 Chirality : 0.043 0.158 2753 Planarity : 0.003 0.047 3174 Dihedral : 5.141 50.139 3286 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.27 % Allowed : 18.73 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.87 (0.32), residues: 263 sheet: 0.21 (0.21), residues: 580 loop : -0.03 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 402 TYR 0.011 0.001 TYR C 313 PHE 0.025 0.001 PHE A 245 TRP 0.014 0.001 TRP C 567 HIS 0.012 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00287 (18301) covalent geometry : angle 0.54146 (24835) SS BOND : bond 0.00328 ( 21) SS BOND : angle 2.49273 ( 42) hydrogen bonds : bond 0.03533 ( 600) hydrogen bonds : angle 5.37915 ( 1440) metal coordination : bond 0.00483 ( 12) link_BETA1-4 : bond 0.00424 ( 20) link_BETA1-4 : angle 1.20265 ( 60) link_BETA1-6 : bond 0.00230 ( 4) link_BETA1-6 : angle 1.26236 ( 12) link_NAG-ASN : bond 0.00117 ( 18) link_NAG-ASN : angle 1.55291 ( 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 503 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 460 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 313 TYR cc_start: 0.8618 (m-80) cc_final: 0.8382 (m-80) REVERT: A 325 GLU cc_start: 0.7536 (mp0) cc_final: 0.7331 (mp0) REVERT: C 251 GLU cc_start: 0.7865 (tt0) cc_final: 0.7647 (tt0) REVERT: C 411 ASP cc_start: 0.7494 (t0) cc_final: 0.7210 (t0) REVERT: D 123 GLN cc_start: 0.8558 (mt0) cc_final: 0.8201 (mt0) REVERT: D 154 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7844 (mt-10) REVERT: D 209 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7588 (mt-10) outliers start: 43 outliers final: 33 residues processed: 475 average time/residue: 0.6836 time to fit residues: 358.2766 Evaluate side-chains 489 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 456 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 288 ASP 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 248 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 A residue 557 CYS Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 318 SER 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 238 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 288 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: 0.3980 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 153 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 370 ASN A 189 HIS C 177 ASN C 182 GLN C 189 HIS C 215 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 = 0.3847 r_free = 0.3847 target = 0.138603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.119959 restraints weight = 22626.598| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.74 r_work: 0.3472 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3313 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= 0.120 Angle : 0.554 12.929 25003 Z= 0.292 Chirality : 0.043 0.159 2753 Planarity : 0.003 0.047 3174 Dihedral : 5.095 50.185 3286 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.01 % Allowed : 19.26 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.14 (0.18), residues: 2117 helix: 0.81 (0.32), residues: 269 sheet: 0.19 (0.21), residues: 575 loop : -0.02 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 402 TYR 0.011 0.001 TYR C 313 PHE 0.020 0.001 PHE C 245 TRP 0.017 0.001 TRP C 567 HIS 0.012 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00277 (18301) covalent geometry : angle 0.53801 (24835) SS BOND : bond 0.00316 ( 21) SS BOND : angle 2.40750 ( 42) hydrogen bonds : bond 0.03490 ( 600) hydrogen bonds : angle 5.34438 ( 1440) metal coordination : bond 0.00475 ( 12) link_BETA1-4 : bond 0.00428 ( 20) link_BETA1-4 : angle 1.19203 ( 60) link_BETA1-6 : bond 0.00231 ( 4) link_BETA1-6 : angle 1.25226 ( 12) link_NAG-ASN : bond 0.00128 ( 18) link_NAG-ASN : angle 1.54316 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9317.03 seconds wall clock time: 158 minutes 38.35 seconds (9518.35 seconds total)