Starting phenix.real_space_refine on Wed Mar 4 22:31:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uab_26419/03_2026/7uab_26419.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uab_26419/03_2026/7uab_26419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uab_26419/03_2026/7uab_26419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uab_26419/03_2026/7uab_26419.map" model { file = "/net/cci-nas-00/data/ceres_data/7uab_26419/03_2026/7uab_26419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uab_26419/03_2026/7uab_26419.cif" } resolution = 3.7 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= 0.031 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 7 9.91 5 Zn 4 6.06 5 S 74 5.16 5 C 10669 2.51 5 N 2808 2.21 5 O 3315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 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: 16877 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3859 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 464} Chain breaks: 10 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3833 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 459} Chain breaks: 11 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4363 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 526} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4365 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 524} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" 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: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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: "F" 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: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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: "I" 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: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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: "K" 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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: "O" 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: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.95, per 1000 atoms: 0.23 Number of scatterers: 16877 At special positions: 0 Unit cell: (100.7, 111.3, 179.14, 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 7 19.99 S 74 16.00 O 3315 8.00 N 2808 7.00 C 10669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 147 " distance=2.05 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 557 " - pdb=" SG CYS A 559 " distance=2.05 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 343 " - pdb=" SG CYS D 431 " distance=2.03 Simple disulfide: pdb=" SG CYS D 557 " - pdb=" SG CYS D 559 " distance=2.02 Simple disulfide: pdb=" SG CYS E 107 " - pdb=" SG CYS E 259 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 269 " - pdb=" SG CYS E 277 " distance=2.04 Simple disulfide: pdb=" SG CYS E 343 " - pdb=" SG CYS E 431 " distance=2.03 Simple disulfide: pdb=" SG CYS E 557 " - pdb=" SG CYS E 559 " distance=2.03 Simple disulfide: pdb=" SG CYS H 107 " - pdb=" SG CYS H 259 " distance=2.03 Simple disulfide: pdb=" SG CYS H 128 " - pdb=" SG CYS H 147 " distance=2.03 Simple disulfide: pdb=" SG CYS H 269 " - pdb=" SG CYS H 277 " distance=2.04 Simple disulfide: pdb=" SG CYS H 343 " - pdb=" SG CYS H 431 " distance=2.03 Simple disulfide: pdb=" SG CYS H 557 " - pdb=" SG CYS H 559 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG G 1 " - " FUC G 3 " " NAG J 1 " - " FUC J 3 " " NAG N 1 " - " FUC N 3 " NAG-ASN " NAG A 701 " - " ASN A 440 " " NAG A 702 " - " ASN A 222 " " NAG B 1 " - " ASN A 140 " " NAG C 1 " - " ASN A 414 " " NAG D 701 " - " ASN D 222 " " NAG D 702 " - " ASN D 440 " " NAG E 701 " - " ASN E 258 " " NAG E 702 " - " ASN E 440 " " NAG F 1 " - " ASN D 140 " " NAG G 1 " - " ASN D 414 " " NAG H 701 " - " ASN H 258 " " NAG I 1 " - " ASN E 140 " " NAG J 1 " - " ASN E 414 " " NAG K 1 " - " ASN E 222 " " NAG L 1 " - " ASN H 222 " " NAG M 1 " - " ASN H 440 " " NAG N 1 " - " ASN H 414 " " NAG O 1 " - " ASN H 140 " Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 760.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 704 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 165 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 159 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 155 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 159 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 165 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 155 " pdb=" ZN E 704 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 159 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 165 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 155 " pdb=" ZN H 703 " pdb="ZN ZN H 703 " - pdb=" NE2 HIS H 159 " pdb="ZN ZN H 703 " - pdb=" NE2 HIS H 165 " pdb="ZN ZN H 703 " - pdb=" NE2 HIS H 155 " 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3806 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 35 sheets defined 22.6% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 88 through 106 Processing helix chain 'A' and resid 149 through 163 removed outlier: 3.919A pdb=" N PHE A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 186 through 192 removed outlier: 4.458A pdb=" N HIS A 189 " --> pdb=" O GLY A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 Processing helix chain 'A' and resid 440 through 448 Processing helix chain 'A' and resid 546 through 551 Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.595A pdb=" N LYS A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 586 Processing helix chain 'A' and resid 597 through 600 Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 54 through 58 Processing helix chain 'D' and resid 88 through 106 Processing helix chain 'D' and resid 149 through 162 Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 187 through 192 Processing helix chain 'D' and resid 246 through 253 Processing helix chain 'D' and resid 440 through 448 Processing helix chain 'D' and resid 516 through 520 removed outlier: 3.647A pdb=" N ARG D 520 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 551 removed outlier: 3.583A pdb=" N VAL D 550 " --> pdb=" O ARG D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 558 Processing helix chain 'D' and resid 573 through 579 removed outlier: 3.608A pdb=" N LYS D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 586 Processing helix chain 'D' and resid 597 through 600 Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 54 through 58 removed outlier: 3.719A pdb=" N GLY E 57 " --> pdb=" O LEU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 106 Processing helix chain 'E' and resid 149 through 162 Processing helix chain 'E' and resid 165 through 169 Processing helix chain 'E' and resid 171 through 174 Processing helix chain 'E' and resid 180 through 183 removed outlier: 3.707A pdb=" N ILE E 183 " --> pdb=" O TRP E 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 180 through 183' Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 232 through 238 removed outlier: 4.052A pdb=" N SER E 237 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 258 Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 411 through 415 removed outlier: 3.722A pdb=" N SER E 415 " --> pdb=" O PRO E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 448 Processing helix chain 'E' and resid 516 through 520 Processing helix chain 'E' and resid 546 through 551 Processing helix chain 'E' and resid 573 through 579 removed outlier: 3.578A pdb=" N ARG E 579 " --> pdb=" O MET E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 removed outlier: 6.909A pdb=" N ASN E 584 " --> pdb=" O PHE E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 600 Processing helix chain 'H' and resid 42 through 50 Processing helix chain 'H' and resid 88 through 106 Processing helix chain 'H' and resid 149 through 162 Processing helix chain 'H' and resid 165 through 170 removed outlier: 6.004A pdb=" N THR H 170 " --> pdb=" O GLN H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 175 removed outlier: 3.865A pdb=" N TYR H 175 " --> pdb=" O ASP H 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 171 through 175' Processing helix chain 'H' and resid 180 through 183 Processing helix chain 'H' and resid 186 through 192 removed outlier: 3.866A pdb=" N HIS H 189 " --> pdb=" O GLY H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 238 removed outlier: 4.244A pdb=" N SER H 237 " --> pdb=" O GLU H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 258 Processing helix chain 'H' and resid 275 through 279 Processing helix chain 'H' and resid 411 through 415 removed outlier: 3.883A pdb=" N SER H 415 " --> pdb=" O PRO H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 448 Processing helix chain 'H' and resid 546 through 551 removed outlier: 3.918A pdb=" N VAL H 550 " --> pdb=" O ARG H 546 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 578 removed outlier: 3.782A pdb=" N ARG H 578 " --> pdb=" O GLN H 574 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 586 Processing helix chain 'H' and resid 597 through 600 Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 112 removed outlier: 5.960A pdb=" N ILE A 79 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N PHE A 122 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE A 82 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 269 Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 269 removed outlier: 5.616A pdb=" N LEU A 421 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS A 349 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP A 423 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE A 347 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.188A pdb=" N VAL A 362 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LYS A 376 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG A 364 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU A 374 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 434 through 438 Processing sheet with id=AA6, first strand: chain 'A' and resid 454 through 455 Processing sheet with id=AA7, first strand: chain 'A' and resid 454 through 455 removed outlier: 3.788A pdb=" N ILE A 571 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU A 484 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLY A 569 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N PHE A 486 " --> pdb=" O TRP A 567 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N TRP A 567 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL A 488 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N LEU A 565 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 552 through 554 Processing sheet with id=AA9, first strand: chain 'D' and resid 110 through 112 removed outlier: 5.815A pdb=" N ILE D 79 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N PHE D 122 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE D 82 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 121 " --> pdb=" O GLN D 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 265 through 269 Processing sheet with id=AB2, first strand: chain 'D' and resid 265 through 269 removed outlier: 5.515A pdb=" N LEU D 421 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS D 349 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP D 423 " --> pdb=" O PHE D 347 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE D 347 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 327 through 330 removed outlier: 6.213A pdb=" N VAL D 362 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS D 376 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU D 374 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 434 through 438 Processing sheet with id=AB5, first strand: chain 'D' and resid 454 through 455 Processing sheet with id=AB6, first strand: chain 'D' and resid 454 through 455 removed outlier: 3.913A pdb=" N GLY D 466 " --> pdb=" O CYS D 489 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU D 482 " --> pdb=" O GLY D 569 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY D 569 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 484 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 552 through 554 Processing sheet with id=AB8, first strand: chain 'E' and resid 110 through 112 removed outlier: 5.942A pdb=" N ILE E 79 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N PHE E 122 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE E 82 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 176 through 178 Processing sheet with id=AC1, first strand: chain 'E' and resid 265 through 269 Processing sheet with id=AC2, first strand: chain 'E' and resid 265 through 269 removed outlier: 5.629A pdb=" N LEU E 421 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LYS E 349 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP E 423 " --> pdb=" O PHE E 347 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE E 347 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 280 through 281 removed outlier: 3.536A pdb=" N ARG E 357 " --> pdb=" O THR E 408 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL E 362 " --> pdb=" O LYS E 376 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS E 376 " --> pdb=" O VAL E 362 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG E 364 " --> pdb=" O LEU E 374 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU E 374 " --> pdb=" O ARG E 364 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 434 through 438 Processing sheet with id=AC5, first strand: chain 'E' and resid 454 through 455 Processing sheet with id=AC6, first strand: chain 'E' and resid 454 through 455 removed outlier: 7.522A pdb=" N LEU E 484 " --> pdb=" O GLY E 569 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY E 569 " --> pdb=" O LEU E 484 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE E 486 " --> pdb=" O TRP E 567 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N TRP E 567 " --> pdb=" O PHE E 486 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N VAL E 488 " --> pdb=" O LEU E 565 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N LEU E 565 " --> pdb=" O VAL E 488 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 552 through 554 Processing sheet with id=AC8, first strand: chain 'H' and resid 59 through 60 Processing sheet with id=AC9, first strand: chain 'H' and resid 110 through 112 removed outlier: 7.843A pdb=" N PHE H 122 " --> pdb=" O PRO H 80 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE H 82 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 176 through 178 Processing sheet with id=AD2, first strand: chain 'H' and resid 265 through 269 removed outlier: 3.605A pdb=" N ASP H 267 " --> pdb=" O LEU H 426 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 265 through 269 removed outlier: 3.605A pdb=" N ASP H 267 " --> pdb=" O LEU H 426 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU H 421 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LYS H 349 " --> pdb=" O LEU H 421 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASP H 423 " --> pdb=" O PHE H 347 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE H 347 " --> pdb=" O ASP H 423 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 280 through 281 removed outlier: 6.838A pdb=" N LEU H 358 " --> pdb=" O THR H 379 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR H 379 " --> pdb=" O LEU H 358 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL H 360 " --> pdb=" O VAL H 377 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 434 through 438 Processing sheet with id=AD6, first strand: chain 'H' and resid 454 through 455 Processing sheet with id=AD7, first strand: chain 'H' and resid 454 through 455 removed outlier: 4.076A pdb=" N GLY H 466 " --> pdb=" O CYS H 489 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE H 571 " --> pdb=" O LEU H 482 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 552 through 554 583 hydrogen bonds defined for protein. 1413 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: 3.40 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3250 1.32 - 1.45: 4617 1.45 - 1.57: 9286 1.57 - 1.70: 0 1.70 - 1.83: 106 Bond restraints: 17259 Sorted by residual: bond pdb=" C GLY A 162 " pdb=" N PHE A 163 " ideal model delta sigma weight residual 1.331 1.244 0.087 1.23e-02 6.61e+03 4.95e+01 bond pdb=" C PHE A 163 " pdb=" N TYR A 164 " ideal model delta sigma weight residual 1.331 1.257 0.074 1.41e-02 5.03e+03 2.72e+01 bond pdb=" N ASP E 58 " pdb=" CA ASP E 58 " ideal model delta sigma weight residual 1.458 1.500 -0.041 9.00e-03 1.23e+04 2.13e+01 bond pdb=" N ASP A 58 " pdb=" CA ASP A 58 " ideal model delta sigma weight residual 1.458 1.499 -0.041 9.00e-03 1.23e+04 2.03e+01 bond pdb=" N ASP D 58 " pdb=" CA ASP D 58 " ideal model delta sigma weight residual 1.458 1.503 -0.045 1.00e-02 1.00e+04 2.00e+01 ... (remaining 17254 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 17661 1.99 - 3.97: 5200 3.97 - 5.96: 463 5.96 - 7.95: 37 7.95 - 9.93: 5 Bond angle restraints: 23366 Sorted by residual: angle pdb=" CA PHE D 590 " pdb=" CB PHE D 590 " pdb=" CG PHE D 590 " ideal model delta sigma weight residual 113.80 120.70 -6.90 1.00e+00 1.00e+00 4.77e+01 angle pdb=" N LEU A 211 " pdb=" CA LEU A 211 " pdb=" C LEU A 211 " ideal model delta sigma weight residual 111.28 103.77 7.51 1.09e+00 8.42e-01 4.74e+01 angle pdb=" CA PHE E 590 " pdb=" CB PHE E 590 " pdb=" CG PHE E 590 " ideal model delta sigma weight residual 113.80 120.43 -6.63 1.00e+00 1.00e+00 4.40e+01 angle pdb=" N GLU A 166 " pdb=" CA GLU A 166 " pdb=" C GLU A 166 " ideal model delta sigma weight residual 113.15 106.42 6.73 1.19e+00 7.06e-01 3.20e+01 angle pdb=" CA ASP D 564 " pdb=" CB ASP D 564 " pdb=" CG ASP D 564 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.00e+00 1.00e+00 3.12e+01 ... (remaining 23361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.34: 10014 22.34 - 44.68: 393 44.68 - 67.03: 85 67.03 - 89.37: 24 89.37 - 111.71: 17 Dihedral angle restraints: 10533 sinusoidal: 4637 harmonic: 5896 Sorted by residual: dihedral pdb=" C THR D 73 " pdb=" N THR D 73 " pdb=" CA THR D 73 " pdb=" CB THR D 73 " ideal model delta harmonic sigma weight residual -122.00 -137.08 15.08 0 2.50e+00 1.60e-01 3.64e+01 dihedral pdb=" N THR D 73 " pdb=" C THR D 73 " pdb=" CA THR D 73 " pdb=" CB THR D 73 " ideal model delta harmonic sigma weight residual 123.40 138.41 -15.01 0 2.50e+00 1.60e-01 3.60e+01 dihedral pdb=" CB CYS D 128 " pdb=" SG CYS D 128 " pdb=" SG CYS D 147 " pdb=" CB CYS D 147 " ideal model delta sinusoidal sigma weight residual -86.00 -135.90 49.90 1 1.00e+01 1.00e-02 3.42e+01 ... (remaining 10530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 2249 0.144 - 0.288: 322 0.288 - 0.432: 25 0.432 - 0.577: 4 0.577 - 0.721: 3 Chirality restraints: 2603 Sorted by residual: chirality pdb=" C1 FUC G 3 " pdb=" O6 NAG G 1 " pdb=" C2 FUC G 3 " pdb=" O5 FUC G 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 8.98e+02 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.47e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.17e+01 ... (remaining 2600 not shown) Planarity restraints: 2994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 701 " 0.365 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C7 NAG E 701 " -0.097 2.00e-02 2.50e+03 pdb=" C8 NAG E 701 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG E 701 " -0.540 2.00e-02 2.50e+03 pdb=" O7 NAG E 701 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.331 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG C 1 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.041 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.500 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 702 " -0.319 2.00e-02 2.50e+03 2.72e-01 9.22e+02 pdb=" C7 NAG E 702 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG E 702 " -0.177 2.00e-02 2.50e+03 pdb=" N2 NAG E 702 " 0.475 2.00e-02 2.50e+03 pdb=" O7 NAG E 702 " -0.059 2.00e-02 2.50e+03 ... (remaining 2991 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 3 2.01 - 2.74: 485 2.74 - 3.46: 22867 3.46 - 4.18: 42005 4.18 - 4.90: 70284 Nonbonded interactions: 135644 Sorted by model distance: nonbonded pdb=" OD2 ASP H 58 " pdb="ZN ZN H 703 " model vdw 1.293 2.230 nonbonded pdb=" OD1 ASP E 58 " pdb="ZN ZN E 704 " model vdw 1.869 2.230 nonbonded pdb=" OD1 ASP D 58 " pdb="ZN ZN D 703 " model vdw 1.886 2.230 nonbonded pdb=" OD1 ASP A 58 " pdb="ZN ZN A 704 " model vdw 2.042 2.230 nonbonded pdb=" OD2 ASP A 58 " pdb="ZN ZN A 704 " model vdw 2.059 2.230 ... (remaining 135639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 62 or resid 72 through 168 or resid 178 through \ 193 or resid 210 through 213 or (resid 214 and (name N or name CA or name C or \ name O or name CB )) or resid 215 through 241 or (resid 242 and (name N or name \ CA or name C or name O or name CB )) or resid 243 through 272 or resid 284 throu \ gh 294 or resid 299 through 330 or resid 337 through 457 or (resid 458 and (name \ N or name CA or name C or name O or name CB )) or resid 459 through 560 or (res \ id 561 and (name N or name CA or name C or name O or name CB )) or resid 562 thr \ ough 577 or (resid 578 and (name N or name CA or name C or name O or name CB )) \ or resid 579 through 701)) selection = (chain 'D' and (resid 40 through 168 or resid 178 through 193 or resid 210 throu \ gh 228 or resid 236 through 241 or (resid 242 and (name N or name CA or name C o \ r name O or name CB )) or resid 243 through 252 or resid 263 through 401 or (res \ id 402 and (name N or name CA or name C or name O or name CB )) or resid 403 thr \ ough 452 or (resid 453 through 455 and (name N or name CA or name C or name O or \ name CB )) or resid 456 through 457 or (resid 458 and (name N or name CA or nam \ e C or name O or name CB )) or resid 459 through 545 or (resid 546 and (name N o \ r name CA or name C or name O or name CB )) or resid 547 through 548 or (resid 5 \ 49 and (name N or name CA or name C or name O or name CB )) or resid 550 through \ 555 or (resid 556 and (name N or name CA or name C or name O or name CB )) or r \ esid 557 or (resid 558 and (name N or name CA or name C or name O or name CB )) \ or resid 559 through 701)) selection = (chain 'E' and (resid 40 through 168 or resid 178 through 193 or resid 210 throu \ gh 213 or (resid 214 and (name N or name CA or name C or name O or name CB )) or \ resid 215 through 228 or resid 236 through 252 or resid 263 through 272 or resi \ d 284 through 294 or resid 299 through 303 or resid 313 through 330 or resid 337 \ through 401 or (resid 402 and (name N or name CA or name C or name O or name CB \ )) or resid 403 through 452 or (resid 453 through 455 and (name N or name CA or \ name C or name O or name CB )) or resid 456 through 475 or resid 479 through 54 \ 5 or (resid 546 and (name N or name CA or name C or name O or name CB )) or resi \ d 547 through 555 or (resid 556 and (name N or name CA or name C or name O or na \ me CB )) or resid 557 or (resid 558 and (name N or name CA or name C or name O o \ r name CB )) or resid 559 through 577 or (resid 578 and (name N or name CA or na \ me C or name O or name CB )) or resid 579 through 701)) selection = (chain 'H' and (resid 40 through 168 or resid 178 through 193 or resid 210 throu \ gh 213 or (resid 214 and (name N or name CA or name C or name O or name CB )) or \ resid 215 through 228 or resid 236 through 241 or (resid 242 and (name N or nam \ e CA or name C or name O or name CB )) or resid 243 through 252 or resid 263 thr \ ough 272 or resid 284 through 294 or resid 299 through 303 or resid 313 through \ 330 or resid 337 through 401 or (resid 402 and (name N or name CA or name C or n \ ame O or name CB )) or resid 403 through 452 or (resid 453 through 455 and (name \ N or name CA or name C or name O or name CB )) or resid 456 through 457 or (res \ id 458 and (name N or name CA or name C or name O or name CB )) or resid 459 thr \ ough 475 or resid 479 through 545 or (resid 546 and (name N or name CA or name C \ or name O or name CB )) or resid 547 through 555 or (resid 556 and (name N or n \ ame CA or name C or name O or name CB )) or resid 557 or (resid 558 and (name N \ or name CA or name C or name O or name CB )) or resid 559 through 577 or (resid \ 578 and (name N or name CA or name C or name O or name CB )) or resid 579 throug \ h 701)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'J' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.790 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 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 : 0.015 0.547 17320 Z= 0.829 Angle : 1.735 11.696 23497 Z= 1.175 Chirality : 0.104 0.721 2603 Planarity : 0.019 0.308 2976 Dihedral : 13.984 111.711 6679 Min Nonbonded Distance : 1.293 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.99 % Favored : 95.96 % Rotamer: Outliers : 0.44 % Allowed : 4.44 % Favored : 95.12 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 12.90 % 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: -0.57 (0.17), residues: 1978 helix: -0.60 (0.27), residues: 272 sheet: 0.12 (0.22), residues: 530 loop : -0.50 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 255 TYR 0.087 0.011 TYR D 460 PHE 0.090 0.012 PHE E 163 TRP 0.057 0.011 TRP E 361 HIS 0.022 0.003 HIS E 165 Details of bonding type rmsd covalent geometry : bond 0.01251 (17259) covalent geometry : angle 1.72384 (23366) SS BOND : bond 0.00757 ( 16) SS BOND : angle 2.22841 ( 32) hydrogen bonds : bond 0.18164 ( 560) hydrogen bonds : angle 7.16565 ( 1413) metal coordination : bond 0.32702 ( 12) link_BETA1-4 : bond 0.00922 ( 11) link_BETA1-4 : angle 2.54718 ( 33) link_BETA1-6 : bond 0.00410 ( 4) link_BETA1-6 : angle 2.34084 ( 12) link_NAG-ASN : bond 0.01031 ( 18) link_NAG-ASN : angle 4.00967 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 758 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8065 (mt) cc_final: 0.7845 (mm) REVERT: A 113 TYR cc_start: 0.7328 (t80) cc_final: 0.7066 (t80) REVERT: A 121 ILE cc_start: 0.7769 (tt) cc_final: 0.7156 (pt) REVERT: A 141 ILE cc_start: 0.8237 (mt) cc_final: 0.8019 (mm) REVERT: A 154 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6201 (mt-10) REVERT: A 156 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6040 (mm-30) REVERT: A 212 MET cc_start: 0.7130 (mmm) cc_final: 0.6772 (mmm) REVERT: A 302 HIS cc_start: 0.8078 (t-90) cc_final: 0.7709 (t70) REVERT: A 314 PHE cc_start: 0.8142 (p90) cc_final: 0.7692 (p90) REVERT: A 315 MET cc_start: 0.6592 (mmm) cc_final: 0.5505 (mmm) REVERT: A 345 GLN cc_start: 0.7966 (tt0) cc_final: 0.7453 (tt0) REVERT: A 347 PHE cc_start: 0.8268 (m-80) cc_final: 0.8055 (m-80) REVERT: A 348 TYR cc_start: 0.7721 (p90) cc_final: 0.7331 (p90) REVERT: A 351 THR cc_start: 0.7209 (p) cc_final: 0.6984 (t) REVERT: A 375 VAL cc_start: 0.7962 (t) cc_final: 0.7543 (m) REVERT: A 376 LYS cc_start: 0.7935 (tttt) cc_final: 0.7719 (tttt) REVERT: A 385 ASP cc_start: 0.6361 (t0) cc_final: 0.6153 (t0) REVERT: A 392 HIS cc_start: 0.7942 (m90) cc_final: 0.7274 (m90) REVERT: A 396 LYS cc_start: 0.7913 (mttt) cc_final: 0.7679 (mttt) REVERT: A 423 ASP cc_start: 0.6907 (m-30) cc_final: 0.6533 (m-30) REVERT: A 438 VAL cc_start: 0.8204 (t) cc_final: 0.7803 (p) REVERT: A 447 ASN cc_start: 0.7322 (m-40) cc_final: 0.7013 (m-40) REVERT: A 465 TYR cc_start: 0.7788 (m-80) cc_final: 0.7316 (m-80) REVERT: A 474 ASN cc_start: 0.7510 (m-40) cc_final: 0.7084 (m-40) REVERT: A 521 MET cc_start: 0.6803 (mtp) cc_final: 0.6419 (mtp) REVERT: A 529 THR cc_start: 0.7744 (p) cc_final: 0.7500 (p) REVERT: A 575 MET cc_start: 0.6999 (tpp) cc_final: 0.6607 (tpp) REVERT: A 583 LYS cc_start: 0.7851 (tptt) cc_final: 0.7544 (tptt) REVERT: A 597 THR cc_start: 0.7781 (m) cc_final: 0.7441 (p) REVERT: A 598 HIS cc_start: 0.8192 (p-80) cc_final: 0.7963 (p90) REVERT: D 45 GLU cc_start: 0.7811 (tt0) cc_final: 0.7326 (tt0) REVERT: D 143 ILE cc_start: 0.7405 (mm) cc_final: 0.7117 (mm) REVERT: D 156 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6430 (mm-30) REVERT: D 212 MET cc_start: 0.6127 (mmm) cc_final: 0.5805 (mmm) REVERT: D 244 ASP cc_start: 0.7074 (t70) cc_final: 0.6497 (t70) REVERT: D 270 THR cc_start: 0.7189 (p) cc_final: 0.6895 (t) REVERT: D 285 ASP cc_start: 0.4933 (p0) cc_final: 0.4587 (p0) REVERT: D 287 THR cc_start: 0.7048 (t) cc_final: 0.6742 (m) REVERT: D 315 MET cc_start: 0.6417 (mmm) cc_final: 0.6152 (mmm) REVERT: D 349 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7949 (ttpp) REVERT: D 355 SER cc_start: 0.7711 (m) cc_final: 0.7472 (p) REVERT: D 356 ASP cc_start: 0.6556 (m-30) cc_final: 0.6350 (m-30) REVERT: D 363 ARG cc_start: 0.7557 (ttm170) cc_final: 0.7276 (ttp-170) REVERT: D 373 LYS cc_start: 0.8274 (tttt) cc_final: 0.7781 (ttmm) REVERT: D 387 ASN cc_start: 0.7488 (m-40) cc_final: 0.7015 (m-40) REVERT: D 393 VAL cc_start: 0.8012 (t) cc_final: 0.7768 (p) REVERT: D 399 GLN cc_start: 0.6842 (mt0) cc_final: 0.6633 (mt0) REVERT: D 400 LYS cc_start: 0.7274 (pttt) cc_final: 0.7016 (pttt) REVERT: D 421 LEU cc_start: 0.7899 (mt) cc_final: 0.7598 (mt) REVERT: D 442 SER cc_start: 0.7914 (m) cc_final: 0.7097 (p) REVERT: D 465 TYR cc_start: 0.7851 (m-80) cc_final: 0.7288 (m-80) REVERT: D 481 TYR cc_start: 0.6615 (m-80) cc_final: 0.6408 (m-80) REVERT: D 497 LEU cc_start: 0.8118 (mt) cc_final: 0.7853 (mt) REVERT: D 512 ASP cc_start: 0.7319 (t0) cc_final: 0.7020 (t0) REVERT: D 531 LYS cc_start: 0.7706 (mttp) cc_final: 0.7234 (mttp) REVERT: D 573 HIS cc_start: 0.7122 (m170) cc_final: 0.6834 (m170) REVERT: E 42 ASP cc_start: 0.7020 (t70) cc_final: 0.6494 (t0) REVERT: E 43 ILE cc_start: 0.7758 (mt) cc_final: 0.7397 (mm) REVERT: E 73 THR cc_start: 0.7471 (p) cc_final: 0.6624 (m) REVERT: E 131 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6513 (mt-10) REVERT: E 153 ILE cc_start: 0.7965 (mt) cc_final: 0.7683 (mm) REVERT: E 156 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6329 (mm-30) REVERT: E 168 SER cc_start: 0.7942 (m) cc_final: 0.7425 (t) REVERT: E 212 MET cc_start: 0.6400 (mmm) cc_final: 0.6183 (mmm) REVERT: E 224 SER cc_start: 0.6923 (m) cc_final: 0.6503 (p) REVERT: E 234 GLU cc_start: 0.7302 (mp0) cc_final: 0.7075 (mp0) REVERT: E 241 GLN cc_start: 0.7715 (pp30) cc_final: 0.7322 (pp30) REVERT: E 251 GLU cc_start: 0.7061 (tp30) cc_final: 0.6445 (tp30) REVERT: E 256 MET cc_start: 0.7254 (ttp) cc_final: 0.5649 (ttp) REVERT: E 279 MET cc_start: 0.7387 (mtp) cc_final: 0.7173 (mtp) REVERT: E 301 ASP cc_start: 0.7622 (p0) cc_final: 0.7403 (p0) REVERT: E 303 THR cc_start: 0.8238 (m) cc_final: 0.8004 (t) REVERT: E 304 LEU cc_start: 0.7996 (mt) cc_final: 0.7714 (mt) REVERT: E 315 MET cc_start: 0.7452 (mmm) cc_final: 0.7130 (mmm) REVERT: E 320 SER cc_start: 0.8316 (p) cc_final: 0.7799 (t) REVERT: E 334 ILE cc_start: 0.8015 (mt) cc_final: 0.7751 (mt) REVERT: E 356 ASP cc_start: 0.6779 (m-30) cc_final: 0.6521 (m-30) REVERT: E 412 PRO cc_start: 0.8679 (Cg_endo) cc_final: 0.8456 (Cg_exo) REVERT: E 443 GLN cc_start: 0.8195 (tt0) cc_final: 0.7842 (tt0) REVERT: E 446 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6600 (mt-10) REVERT: E 474 ASN cc_start: 0.7501 (m-40) cc_final: 0.6914 (p0) REVERT: E 486 PHE cc_start: 0.7695 (t80) cc_final: 0.7195 (t80) REVERT: E 504 ARG cc_start: 0.7656 (mpt180) cc_final: 0.7412 (mmt180) REVERT: E 505 GLN cc_start: 0.7754 (tt0) cc_final: 0.7535 (tt0) REVERT: E 521 MET cc_start: 0.7041 (mtp) cc_final: 0.5464 (mtp) REVERT: E 525 MET cc_start: 0.7331 (mmt) cc_final: 0.7035 (mmm) REVERT: E 579 ARG cc_start: 0.6799 (ttt90) cc_final: 0.6004 (mmm-85) REVERT: E 588 ILE cc_start: 0.8260 (mt) cc_final: 0.7731 (tt) REVERT: E 590 PHE cc_start: 0.8271 (m-10) cc_final: 0.8039 (m-10) REVERT: H 45 GLU cc_start: 0.7779 (tt0) cc_final: 0.7409 (tt0) REVERT: H 74 ARG cc_start: 0.6937 (mtt90) cc_final: 0.6394 (mtt-85) REVERT: H 76 THR cc_start: 0.7758 (m) cc_final: 0.7446 (p) REVERT: H 100 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6503 (mm-30) REVERT: H 101 MET cc_start: 0.7331 (mmm) cc_final: 0.7002 (mmm) REVERT: H 102 PHE cc_start: 0.7796 (m-80) cc_final: 0.7546 (m-10) REVERT: H 111 LYS cc_start: 0.7775 (pttt) cc_final: 0.7198 (pttt) REVERT: H 113 TYR cc_start: 0.7054 (t80) cc_final: 0.6776 (t80) REVERT: H 130 SER cc_start: 0.8405 (t) cc_final: 0.6827 (p) REVERT: H 131 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6282 (mt-10) REVERT: H 134 ASP cc_start: 0.6941 (t0) cc_final: 0.6274 (t0) REVERT: H 156 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6120 (mm-30) REVERT: H 173 ASP cc_start: 0.7520 (m-30) cc_final: 0.7192 (m-30) REVERT: H 207 ASP cc_start: 0.6266 (t0) cc_final: 0.6011 (t0) REVERT: H 209 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6893 (mt-10) REVERT: H 212 MET cc_start: 0.7026 (mmm) cc_final: 0.6805 (mmm) REVERT: H 218 SER cc_start: 0.7816 (m) cc_final: 0.7591 (p) REVERT: H 241 GLN cc_start: 0.7445 (pp30) cc_final: 0.7048 (pp30) REVERT: H 256 MET cc_start: 0.7291 (ttp) cc_final: 0.6629 (ttp) REVERT: H 267 ASP cc_start: 0.7113 (t0) cc_final: 0.6896 (t0) REVERT: H 275 ASN cc_start: 0.7687 (p0) cc_final: 0.7387 (p0) REVERT: H 283 THR cc_start: 0.7401 (p) cc_final: 0.7182 (t) REVERT: H 313 TYR cc_start: 0.7494 (m-80) cc_final: 0.7257 (m-80) REVERT: H 315 MET cc_start: 0.7259 (mmm) cc_final: 0.6874 (mmm) REVERT: H 333 ARG cc_start: 0.7704 (ptt90) cc_final: 0.7494 (ptt90) REVERT: H 336 TYR cc_start: 0.8176 (m-80) cc_final: 0.7897 (m-80) REVERT: H 338 LYS cc_start: 0.7878 (mttt) cc_final: 0.7567 (mttt) REVERT: H 341 GLN cc_start: 0.7706 (tt0) cc_final: 0.7492 (tt0) REVERT: H 342 GLN cc_start: 0.8082 (mp10) cc_final: 0.7846 (mp10) REVERT: H 349 LYS cc_start: 0.8254 (ttpt) cc_final: 0.8034 (ttpt) REVERT: H 364 ARG cc_start: 0.7483 (ptp-170) cc_final: 0.6750 (ptm160) REVERT: H 381 GLN cc_start: 0.6751 (tp40) cc_final: 0.6385 (mm-40) REVERT: H 394 VAL cc_start: 0.8477 (t) cc_final: 0.8165 (m) REVERT: H 404 LEU cc_start: 0.8454 (mp) cc_final: 0.7977 (mp) REVERT: H 419 ILE cc_start: 0.8366 (mt) cc_final: 0.8158 (mm) REVERT: H 425 THR cc_start: 0.8078 (m) cc_final: 0.7858 (p) REVERT: H 438 VAL cc_start: 0.8372 (t) cc_final: 0.8024 (p) REVERT: H 463 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6736 (mt-10) REVERT: H 471 LEU cc_start: 0.8046 (tp) cc_final: 0.7563 (tp) REVERT: H 489 CYS cc_start: 0.7896 (m) cc_final: 0.7687 (m) REVERT: H 498 GLU cc_start: 0.6815 (tt0) cc_final: 0.6487 (tt0) REVERT: H 502 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6713 (mt-10) REVERT: H 504 ARG cc_start: 0.7870 (mpt180) cc_final: 0.7318 (mmt180) REVERT: H 510 ILE cc_start: 0.8384 (mt) cc_final: 0.8061 (mm) REVERT: H 521 MET cc_start: 0.7157 (mtp) cc_final: 0.6565 (mtp) REVERT: H 522 SER cc_start: 0.8281 (m) cc_final: 0.7954 (p) REVERT: H 575 MET cc_start: 0.6491 (tpp) cc_final: 0.6164 (tpp) REVERT: H 581 PHE cc_start: 0.8168 (m-80) cc_final: 0.7852 (m-80) REVERT: H 583 LYS cc_start: 0.7647 (tttp) cc_final: 0.7394 (tttp) REVERT: H 592 ASP cc_start: 0.6747 (m-30) cc_final: 0.6513 (m-30) REVERT: H 593 PHE cc_start: 0.8369 (t80) cc_final: 0.7252 (t80) outliers start: 8 outliers final: 4 residues processed: 763 average time/residue: 0.1360 time to fit residues: 150.9546 Evaluate side-chains 624 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 620 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 TYR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain H residue 140 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 123 GLN A 139 GLN A 189 HIS A 316 GLN A 342 GLN A 381 GLN A 505 GLN A 554 HIS D 86 ASN D 139 GLN D 341 GLN D 345 GLN D 386 HIS D 455 GLN D 474 ASN D 493 ASN E 86 ASN E 135 GLN E 136 HIS E 139 GLN E 182 GLN ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 ASN H 135 GLN H 159 HIS ** H 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.147139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128875 restraints weight = 26408.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133504 restraints weight = 13172.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136556 restraints weight = 7937.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.138580 restraints weight = 5372.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.139926 restraints weight = 3941.066| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.642 17320 Z= 0.224 Angle : 0.683 13.369 23497 Z= 0.356 Chirality : 0.047 0.235 2603 Planarity : 0.004 0.064 2976 Dihedral : 8.923 118.814 2862 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.44 % Allowed : 11.54 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: 0.30 (0.18), residues: 1978 helix: 0.98 (0.30), residues: 288 sheet: 0.56 (0.21), residues: 588 loop : -0.15 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 74 TYR 0.017 0.002 TYR E 465 PHE 0.025 0.002 PHE A 527 TRP 0.021 0.002 TRP A 361 HIS 0.012 0.002 HIS A 554 Details of bonding type rmsd covalent geometry : bond 0.00329 (17259) covalent geometry : angle 0.65986 (23366) SS BOND : bond 0.00313 ( 16) SS BOND : angle 1.68187 ( 32) hydrogen bonds : bond 0.05167 ( 560) hydrogen bonds : angle 5.64414 ( 1413) metal coordination : bond 0.18661 ( 12) link_BETA1-4 : bond 0.00473 ( 11) link_BETA1-4 : angle 1.82244 ( 33) link_BETA1-6 : bond 0.00557 ( 4) link_BETA1-6 : angle 2.12060 ( 12) link_NAG-ASN : bond 0.00360 ( 18) link_NAG-ASN : angle 3.17847 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 632 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ILE cc_start: 0.7703 (mt) cc_final: 0.7354 (mm) REVERT: A 113 TYR cc_start: 0.7309 (t80) cc_final: 0.7057 (t80) REVERT: A 121 ILE cc_start: 0.7718 (tt) cc_final: 0.7101 (pt) REVERT: A 132 VAL cc_start: 0.7783 (p) cc_final: 0.7583 (t) REVERT: A 141 ILE cc_start: 0.8110 (mt) cc_final: 0.7825 (mm) REVERT: A 156 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6293 (mm-30) REVERT: A 188 GLN cc_start: 0.7919 (pm20) cc_final: 0.7545 (pm20) REVERT: A 271 PHE cc_start: 0.8092 (m-10) cc_final: 0.7404 (m-10) REVERT: A 293 ASP cc_start: 0.6264 (p0) cc_final: 0.5727 (p0) REVERT: A 314 PHE cc_start: 0.8010 (p90) cc_final: 0.7420 (p90) REVERT: A 315 MET cc_start: 0.6423 (mmm) cc_final: 0.5553 (mmm) REVERT: A 317 PHE cc_start: 0.7805 (t80) cc_final: 0.7284 (t80) REVERT: A 345 GLN cc_start: 0.8002 (tt0) cc_final: 0.7669 (tt0) REVERT: A 359 VAL cc_start: 0.8207 (t) cc_final: 0.7867 (m) REVERT: A 363 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7506 (ttp-170) REVERT: A 372 ARG cc_start: 0.7148 (ttp-110) cc_final: 0.6762 (ptm-80) REVERT: A 375 VAL cc_start: 0.8053 (t) cc_final: 0.7670 (p) REVERT: A 385 ASP cc_start: 0.6389 (t0) cc_final: 0.6135 (t0) REVERT: A 396 LYS cc_start: 0.7975 (mttt) cc_final: 0.7391 (mttt) REVERT: A 447 ASN cc_start: 0.7492 (m-40) cc_final: 0.7185 (m-40) REVERT: A 465 TYR cc_start: 0.7720 (m-80) cc_final: 0.7481 (m-80) REVERT: A 474 ASN cc_start: 0.7817 (m-40) cc_final: 0.7536 (m-40) REVERT: A 498 GLU cc_start: 0.6652 (tt0) cc_final: 0.6427 (tt0) REVERT: A 502 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6584 (mt-10) REVERT: A 505 GLN cc_start: 0.7857 (tt0) cc_final: 0.7575 (tt0) REVERT: A 527 PHE cc_start: 0.8036 (p90) cc_final: 0.7586 (p90) REVERT: A 529 THR cc_start: 0.7924 (p) cc_final: 0.7670 (p) REVERT: A 575 MET cc_start: 0.6603 (tpp) cc_final: 0.6251 (tpp) REVERT: A 583 LYS cc_start: 0.7827 (tptt) cc_final: 0.7448 (tptt) REVERT: A 585 ASP cc_start: 0.6383 (t0) cc_final: 0.6072 (t0) REVERT: A 586 ASP cc_start: 0.7378 (m-30) cc_final: 0.7178 (m-30) REVERT: D 135 GLN cc_start: 0.7253 (mm-40) cc_final: 0.6983 (mm-40) REVERT: D 141 ILE cc_start: 0.7836 (mt) cc_final: 0.7461 (mm) REVERT: D 163 PHE cc_start: 0.7015 (m-80) cc_final: 0.6416 (m-80) REVERT: D 212 MET cc_start: 0.6344 (mmm) cc_final: 0.5857 (mmm) REVERT: D 242 ARG cc_start: 0.7121 (mmt180) cc_final: 0.6706 (mmt-90) REVERT: D 244 ASP cc_start: 0.6950 (t70) cc_final: 0.6517 (t70) REVERT: D 252 ARG cc_start: 0.7522 (mtp180) cc_final: 0.6761 (mtp180) REVERT: D 270 THR cc_start: 0.7338 (p) cc_final: 0.7096 (t) REVERT: D 285 ASP cc_start: 0.5087 (p0) cc_final: 0.4682 (p0) REVERT: D 287 THR cc_start: 0.7310 (t) cc_final: 0.6837 (m) REVERT: D 292 GLN cc_start: 0.7292 (mm110) cc_final: 0.7091 (tp40) REVERT: D 330 LEU cc_start: 0.7561 (mt) cc_final: 0.7032 (mt) REVERT: D 355 SER cc_start: 0.7731 (m) cc_final: 0.7421 (p) REVERT: D 393 VAL cc_start: 0.7877 (t) cc_final: 0.7545 (p) REVERT: D 396 LYS cc_start: 0.7742 (mttt) cc_final: 0.7423 (mttt) REVERT: D 428 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6476 (mt-10) REVERT: D 445 LEU cc_start: 0.8260 (tp) cc_final: 0.8011 (mt) REVERT: D 453 LYS cc_start: 0.6824 (pttt) cc_final: 0.6050 (pttt) REVERT: D 460 TYR cc_start: 0.8371 (m-80) cc_final: 0.8031 (m-10) REVERT: D 469 VAL cc_start: 0.7700 (t) cc_final: 0.7480 (p) REVERT: D 481 TYR cc_start: 0.6769 (m-80) cc_final: 0.6560 (m-80) REVERT: D 486 PHE cc_start: 0.7958 (t80) cc_final: 0.7394 (t80) REVERT: D 502 GLU cc_start: 0.7157 (mt-10) cc_final: 0.5881 (mt-10) REVERT: D 512 ASP cc_start: 0.7120 (t0) cc_final: 0.6849 (t0) REVERT: D 531 LYS cc_start: 0.7672 (mttp) cc_final: 0.7095 (mttp) REVERT: D 573 HIS cc_start: 0.7209 (m170) cc_final: 0.6210 (m170) REVERT: D 577 LYS cc_start: 0.7413 (mmtt) cc_final: 0.7176 (mmtt) REVERT: E 73 THR cc_start: 0.7703 (p) cc_final: 0.6934 (m) REVERT: E 101 MET cc_start: 0.7725 (mmm) cc_final: 0.7352 (mmm) REVERT: E 131 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6489 (mt-10) REVERT: E 153 ILE cc_start: 0.7856 (mt) cc_final: 0.7606 (mm) REVERT: E 156 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6424 (mm-30) REVERT: E 182 GLN cc_start: 0.7368 (mm110) cc_final: 0.7138 (mm-40) REVERT: E 215 GLN cc_start: 0.7276 (mt0) cc_final: 0.6798 (mt0) REVERT: E 234 GLU cc_start: 0.7320 (mp0) cc_final: 0.7085 (mp0) REVERT: E 241 GLN cc_start: 0.7849 (pp30) cc_final: 0.7492 (pp30) REVERT: E 256 MET cc_start: 0.6788 (ttp) cc_final: 0.6562 (ttp) REVERT: E 265 LEU cc_start: 0.8280 (tp) cc_final: 0.7982 (tp) REVERT: E 266 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8043 (mm) REVERT: E 267 ASP cc_start: 0.7260 (t0) cc_final: 0.6610 (t0) REVERT: E 279 MET cc_start: 0.7571 (mtp) cc_final: 0.7361 (mtp) REVERT: E 299 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6298 (mm-30) REVERT: E 303 THR cc_start: 0.8399 (m) cc_final: 0.7840 (t) REVERT: E 304 LEU cc_start: 0.7973 (mt) cc_final: 0.7652 (mt) REVERT: E 315 MET cc_start: 0.7320 (mmm) cc_final: 0.6910 (mmm) REVERT: E 336 TYR cc_start: 0.8028 (m-80) cc_final: 0.7813 (m-80) REVERT: E 350 MET cc_start: 0.7437 (mtp) cc_final: 0.7231 (mtm) REVERT: E 400 LYS cc_start: 0.7991 (pttt) cc_final: 0.7594 (ptpp) REVERT: E 409 LYS cc_start: 0.8341 (mtpt) cc_final: 0.7592 (ttpp) REVERT: E 412 PRO cc_start: 0.8791 (Cg_endo) cc_final: 0.8386 (Cg_exo) REVERT: E 428 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7089 (mt-10) REVERT: E 463 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6545 (mt-10) REVERT: E 474 ASN cc_start: 0.7697 (m-40) cc_final: 0.7253 (m-40) REVERT: E 486 PHE cc_start: 0.7772 (t80) cc_final: 0.7308 (t80) REVERT: E 518 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.7749 (mtp-110) REVERT: E 521 MET cc_start: 0.7079 (mtp) cc_final: 0.6366 (mtp) REVERT: E 525 MET cc_start: 0.7260 (mmt) cc_final: 0.6857 (mmt) REVERT: E 577 LYS cc_start: 0.7701 (mtpp) cc_final: 0.7462 (mtpp) REVERT: E 588 ILE cc_start: 0.8390 (mt) cc_final: 0.7895 (tt) REVERT: H 74 ARG cc_start: 0.7040 (mtt90) cc_final: 0.6462 (mtt-85) REVERT: H 76 THR cc_start: 0.7688 (m) cc_final: 0.7366 (p) REVERT: H 81 TYR cc_start: 0.7910 (p90) cc_final: 0.7308 (p90) REVERT: H 100 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6903 (mm-30) REVERT: H 101 MET cc_start: 0.7499 (mmm) cc_final: 0.7218 (mmm) REVERT: H 111 LYS cc_start: 0.7859 (pttt) cc_final: 0.7198 (pttt) REVERT: H 124 GLN cc_start: 0.6986 (tt0) cc_final: 0.6641 (tm-30) REVERT: H 130 SER cc_start: 0.8315 (t) cc_final: 0.6828 (p) REVERT: H 134 ASP cc_start: 0.6847 (t0) cc_final: 0.6620 (t0) REVERT: H 154 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6532 (mt-10) REVERT: H 156 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6143 (mm-30) REVERT: H 173 ASP cc_start: 0.7528 (m-30) cc_final: 0.7248 (m-30) REVERT: H 207 ASP cc_start: 0.6380 (t0) cc_final: 0.6115 (t0) REVERT: H 209 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6921 (mt-10) REVERT: H 212 MET cc_start: 0.7063 (mmm) cc_final: 0.6768 (mmm) REVERT: H 218 SER cc_start: 0.8188 (m) cc_final: 0.7856 (p) REVERT: H 241 GLN cc_start: 0.7693 (pp30) cc_final: 0.7138 (pp30) REVERT: H 252 ARG cc_start: 0.7595 (ttm170) cc_final: 0.7311 (mtm-85) REVERT: H 256 MET cc_start: 0.7395 (ttp) cc_final: 0.6837 (ttp) REVERT: H 275 ASN cc_start: 0.7529 (p0) cc_final: 0.7157 (p0) REVERT: H 303 THR cc_start: 0.8273 (m) cc_final: 0.7717 (t) REVERT: H 313 TYR cc_start: 0.7620 (m-80) cc_final: 0.7387 (m-80) REVERT: H 315 MET cc_start: 0.7296 (mmm) cc_final: 0.6892 (mmm) REVERT: H 331 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6555 (mt-10) REVERT: H 338 LYS cc_start: 0.7907 (mttt) cc_final: 0.7627 (mttt) REVERT: H 349 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7956 (ttpt) REVERT: H 364 ARG cc_start: 0.7668 (ptp-170) cc_final: 0.7228 (ptm160) REVERT: H 381 GLN cc_start: 0.6989 (tp40) cc_final: 0.6600 (mm-40) REVERT: H 394 VAL cc_start: 0.8489 (t) cc_final: 0.8267 (m) REVERT: H 397 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6224 (mm-30) REVERT: H 404 LEU cc_start: 0.8441 (mp) cc_final: 0.7810 (mt) REVERT: H 471 LEU cc_start: 0.7944 (tp) cc_final: 0.7563 (tp) REVERT: H 498 GLU cc_start: 0.7015 (tt0) cc_final: 0.6666 (tt0) REVERT: H 521 MET cc_start: 0.7389 (mtp) cc_final: 0.6833 (mtp) REVERT: H 553 TYR cc_start: 0.6179 (t80) cc_final: 0.5966 (t80) REVERT: H 592 ASP cc_start: 0.6751 (m-30) cc_final: 0.6322 (m-30) REVERT: H 593 PHE cc_start: 0.8004 (t80) cc_final: 0.7430 (t80) outliers start: 44 outliers final: 27 residues processed: 655 average time/residue: 0.1338 time to fit residues: 128.0838 Evaluate side-chains 633 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 605 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 532 SER Chi-restraints excluded: chain H residue 563 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 46 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 136 HIS A 139 GLN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN A 487 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 399 GLN D 443 GLN D 493 ASN E 220 ASN E 268 HIS E 505 GLN H 159 HIS H 177 ASN H 190 ASN H 220 ASN H 302 HIS H 341 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123441 restraints weight = 26688.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128040 restraints weight = 13457.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.131078 restraints weight = 8180.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133011 restraints weight = 5590.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.134442 restraints weight = 4176.437| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.813 17320 Z= 0.291 Angle : 0.637 9.183 23497 Z= 0.337 Chirality : 0.046 0.234 2603 Planarity : 0.004 0.042 2976 Dihedral : 7.018 120.928 2856 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.94 % Allowed : 14.10 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: 0.30 (0.18), residues: 1978 helix: 1.17 (0.30), residues: 295 sheet: 0.65 (0.21), residues: 576 loop : -0.27 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 458 TYR 0.017 0.002 TYR E 403 PHE 0.021 0.002 PHE H 593 TRP 0.020 0.002 TRP A 361 HIS 0.010 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00445 (17259) covalent geometry : angle 0.61685 (23366) SS BOND : bond 0.00328 ( 16) SS BOND : angle 1.21013 ( 32) hydrogen bonds : bond 0.04880 ( 560) hydrogen bonds : angle 5.42481 ( 1413) metal coordination : bond 0.23544 ( 12) link_BETA1-4 : bond 0.00514 ( 11) link_BETA1-4 : angle 1.84788 ( 33) link_BETA1-6 : bond 0.00443 ( 4) link_BETA1-6 : angle 1.52247 ( 12) link_NAG-ASN : bond 0.00459 ( 18) link_NAG-ASN : angle 2.90827 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 637 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.7729 (p0) cc_final: 0.7503 (p0) REVERT: A 113 TYR cc_start: 0.7541 (t80) cc_final: 0.7304 (t80) REVERT: A 121 ILE cc_start: 0.7781 (tt) cc_final: 0.7200 (pt) REVERT: A 123 GLN cc_start: 0.8151 (mt0) cc_final: 0.7856 (tt0) REVERT: A 130 SER cc_start: 0.7507 (t) cc_final: 0.6458 (t) REVERT: A 156 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6505 (mm-30) REVERT: A 271 PHE cc_start: 0.8102 (m-10) cc_final: 0.7793 (m-10) REVERT: A 293 ASP cc_start: 0.6455 (p0) cc_final: 0.5912 (p0) REVERT: A 315 MET cc_start: 0.6435 (mmm) cc_final: 0.5773 (mmm) REVERT: A 345 GLN cc_start: 0.8015 (tt0) cc_final: 0.7777 (tt0) REVERT: A 363 ARG cc_start: 0.7973 (ttm170) cc_final: 0.7600 (ttp-110) REVERT: A 372 ARG cc_start: 0.7159 (ttp-110) cc_final: 0.6676 (ptm-80) REVERT: A 375 VAL cc_start: 0.8097 (t) cc_final: 0.7732 (p) REVERT: A 384 ASP cc_start: 0.5579 (m-30) cc_final: 0.5303 (m-30) REVERT: A 396 LYS cc_start: 0.7833 (mttt) cc_final: 0.7510 (mttt) REVERT: A 443 GLN cc_start: 0.7725 (mp10) cc_final: 0.7233 (mp10) REVERT: A 447 ASN cc_start: 0.7725 (m-40) cc_final: 0.7463 (m-40) REVERT: A 465 TYR cc_start: 0.7869 (m-80) cc_final: 0.7404 (m-80) REVERT: A 471 LEU cc_start: 0.8402 (tp) cc_final: 0.8197 (tp) REVERT: A 474 ASN cc_start: 0.7974 (m-40) cc_final: 0.7773 (m110) REVERT: A 502 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6654 (mt-10) REVERT: A 505 GLN cc_start: 0.7953 (tt0) cc_final: 0.7724 (tt0) REVERT: A 527 PHE cc_start: 0.7934 (p90) cc_final: 0.7682 (p90) REVERT: A 583 LYS cc_start: 0.7859 (tptt) cc_final: 0.7528 (tptt) REVERT: D 45 GLU cc_start: 0.7835 (tt0) cc_final: 0.7351 (tt0) REVERT: D 85 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6961 (t0) REVERT: D 92 LYS cc_start: 0.8212 (mttt) cc_final: 0.7999 (mttt) REVERT: D 105 LYS cc_start: 0.8230 (mttt) cc_final: 0.7620 (mtmt) REVERT: D 135 GLN cc_start: 0.7269 (mm-40) cc_final: 0.6958 (mm-40) REVERT: D 141 ILE cc_start: 0.7902 (mt) cc_final: 0.7549 (mm) REVERT: D 142 SER cc_start: 0.8133 (t) cc_final: 0.7286 (p) REVERT: D 163 PHE cc_start: 0.7120 (m-80) cc_final: 0.6388 (m-80) REVERT: D 212 MET cc_start: 0.6311 (mmm) cc_final: 0.5885 (mmm) REVERT: D 244 ASP cc_start: 0.7013 (t70) cc_final: 0.6443 (t70) REVERT: D 252 ARG cc_start: 0.7589 (mtp180) cc_final: 0.6682 (mtp180) REVERT: D 270 THR cc_start: 0.7357 (p) cc_final: 0.7117 (t) REVERT: D 285 ASP cc_start: 0.5650 (p0) cc_final: 0.5354 (p0) REVERT: D 287 THR cc_start: 0.7412 (t) cc_final: 0.6864 (m) REVERT: D 315 MET cc_start: 0.6542 (mmm) cc_final: 0.6278 (mmm) REVERT: D 330 LEU cc_start: 0.7556 (mt) cc_final: 0.7111 (mt) REVERT: D 339 ARG cc_start: 0.6484 (mtt180) cc_final: 0.6234 (mtt-85) REVERT: D 355 SER cc_start: 0.7709 (m) cc_final: 0.7357 (p) REVERT: D 396 LYS cc_start: 0.7801 (mttt) cc_final: 0.7480 (mttt) REVERT: D 400 LYS cc_start: 0.7839 (pttt) cc_final: 0.7609 (pttt) REVERT: D 405 PHE cc_start: 0.7680 (m-10) cc_final: 0.7458 (m-10) REVERT: D 428 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6304 (mm-30) REVERT: D 441 PHE cc_start: 0.8494 (t80) cc_final: 0.7778 (t80) REVERT: D 445 LEU cc_start: 0.8218 (tp) cc_final: 0.7950 (mt) REVERT: D 446 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6650 (mp0) REVERT: D 453 LYS cc_start: 0.6893 (pttt) cc_final: 0.6571 (pttt) REVERT: D 460 TYR cc_start: 0.8387 (m-80) cc_final: 0.8167 (m-10) REVERT: D 486 PHE cc_start: 0.7931 (t80) cc_final: 0.7457 (t80) REVERT: D 487 HIS cc_start: 0.7752 (p-80) cc_final: 0.7472 (p-80) REVERT: D 502 GLU cc_start: 0.7434 (mt-10) cc_final: 0.5835 (mt-10) REVERT: D 512 ASP cc_start: 0.7083 (t0) cc_final: 0.6828 (t0) REVERT: D 531 LYS cc_start: 0.7879 (mttp) cc_final: 0.7290 (mttp) REVERT: D 546 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7607 (ttm-80) REVERT: D 573 HIS cc_start: 0.7364 (m170) cc_final: 0.6410 (m170) REVERT: D 577 LYS cc_start: 0.7559 (mmtt) cc_final: 0.7298 (mmtt) REVERT: E 74 ARG cc_start: 0.7399 (mtt-85) cc_final: 0.7075 (mtt-85) REVERT: E 111 LYS cc_start: 0.7881 (pttt) cc_final: 0.7596 (ptmt) REVERT: E 131 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6548 (mt-10) REVERT: E 136 HIS cc_start: 0.7333 (m-70) cc_final: 0.6820 (m-70) REVERT: E 143 ILE cc_start: 0.8512 (mm) cc_final: 0.8258 (tp) REVERT: E 167 GLN cc_start: 0.7840 (pm20) cc_final: 0.7609 (pm20) REVERT: E 173 ASP cc_start: 0.7877 (m-30) cc_final: 0.7648 (t0) REVERT: E 215 GLN cc_start: 0.7462 (mt0) cc_final: 0.7013 (mt0) REVERT: E 234 GLU cc_start: 0.7396 (mp0) cc_final: 0.7135 (mp0) REVERT: E 241 GLN cc_start: 0.7955 (pp30) cc_final: 0.7722 (pp30) REVERT: E 251 GLU cc_start: 0.7361 (tp30) cc_final: 0.6735 (tp30) REVERT: E 256 MET cc_start: 0.7179 (ttp) cc_final: 0.6434 (ttp) REVERT: E 267 ASP cc_start: 0.7329 (t0) cc_final: 0.6792 (t0) REVERT: E 279 MET cc_start: 0.7563 (mtp) cc_final: 0.7357 (mtp) REVERT: E 299 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6329 (mt-10) REVERT: E 303 THR cc_start: 0.8359 (m) cc_final: 0.7667 (t) REVERT: E 304 LEU cc_start: 0.8026 (mt) cc_final: 0.7738 (mt) REVERT: E 315 MET cc_start: 0.7206 (mmm) cc_final: 0.6906 (mmm) REVERT: E 320 SER cc_start: 0.8297 (p) cc_final: 0.7896 (t) REVERT: E 326 GLU cc_start: 0.6355 (mt-10) cc_final: 0.6093 (mt-10) REVERT: E 347 PHE cc_start: 0.8278 (m-80) cc_final: 0.8046 (m-80) REVERT: E 400 LYS cc_start: 0.7993 (pttt) cc_final: 0.7665 (ptpp) REVERT: E 409 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7636 (ttpp) REVERT: E 412 PRO cc_start: 0.8759 (Cg_endo) cc_final: 0.8323 (Cg_exo) REVERT: E 428 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7113 (mt-10) REVERT: E 474 ASN cc_start: 0.7982 (m-40) cc_final: 0.7778 (m-40) REVERT: E 484 LEU cc_start: 0.7848 (mt) cc_final: 0.7586 (mm) REVERT: E 486 PHE cc_start: 0.7991 (t80) cc_final: 0.7559 (t80) REVERT: E 504 ARG cc_start: 0.7927 (mmt-90) cc_final: 0.7673 (mmt-90) REVERT: E 518 ARG cc_start: 0.8165 (ttp-110) cc_final: 0.7806 (mtp-110) REVERT: E 521 MET cc_start: 0.7192 (mtp) cc_final: 0.6600 (mtp) REVERT: E 525 MET cc_start: 0.7351 (mmt) cc_final: 0.6923 (mmt) REVERT: E 546 ARG cc_start: 0.7926 (ttm170) cc_final: 0.7615 (ttm-80) REVERT: E 577 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7671 (mtpp) REVERT: E 588 ILE cc_start: 0.8401 (mt) cc_final: 0.7910 (tp) REVERT: H 74 ARG cc_start: 0.7100 (mtt90) cc_final: 0.6609 (mtt-85) REVERT: H 76 THR cc_start: 0.7743 (m) cc_final: 0.7353 (p) REVERT: H 81 TYR cc_start: 0.7964 (p90) cc_final: 0.7302 (p90) REVERT: H 100 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7063 (mm-30) REVERT: H 101 MET cc_start: 0.7523 (mmm) cc_final: 0.7317 (mmm) REVERT: H 102 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: H 111 LYS cc_start: 0.7905 (pttt) cc_final: 0.7204 (pttt) REVERT: H 130 SER cc_start: 0.8473 (t) cc_final: 0.7887 (p) REVERT: H 154 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6650 (mt-10) REVERT: H 173 ASP cc_start: 0.7516 (m-30) cc_final: 0.7252 (m-30) REVERT: H 207 ASP cc_start: 0.6494 (t0) cc_final: 0.6228 (t0) REVERT: H 209 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6955 (mt-10) REVERT: H 241 GLN cc_start: 0.7973 (pp30) cc_final: 0.7507 (pp30) REVERT: H 252 ARG cc_start: 0.7531 (ttm170) cc_final: 0.7276 (mtm-85) REVERT: H 254 ASN cc_start: 0.8076 (m-40) cc_final: 0.7823 (t0) REVERT: H 256 MET cc_start: 0.7496 (ttp) cc_final: 0.6918 (ttp) REVERT: H 275 ASN cc_start: 0.7512 (p0) cc_final: 0.7274 (p0) REVERT: H 303 THR cc_start: 0.8195 (m) cc_final: 0.7536 (t) REVERT: H 315 MET cc_start: 0.7254 (mmm) cc_final: 0.6869 (mmm) REVERT: H 331 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6551 (mt-10) REVERT: H 364 ARG cc_start: 0.7801 (ptp-170) cc_final: 0.7367 (ptm160) REVERT: H 381 GLN cc_start: 0.7335 (tp40) cc_final: 0.6859 (mm-40) REVERT: H 394 VAL cc_start: 0.8605 (t) cc_final: 0.8297 (m) REVERT: H 397 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6258 (mm-30) REVERT: H 404 LEU cc_start: 0.8443 (mp) cc_final: 0.7758 (mp) REVERT: H 432 PRO cc_start: 0.8377 (Cg_endo) cc_final: 0.8149 (Cg_exo) REVERT: H 438 VAL cc_start: 0.8154 (t) cc_final: 0.7851 (p) REVERT: H 471 LEU cc_start: 0.8052 (tp) cc_final: 0.7723 (tp) REVERT: H 498 GLU cc_start: 0.7104 (tt0) cc_final: 0.6705 (tt0) REVERT: H 521 MET cc_start: 0.7447 (mtp) cc_final: 0.6937 (mtp) REVERT: H 522 SER cc_start: 0.8615 (p) cc_final: 0.8397 (p) REVERT: H 575 MET cc_start: 0.6738 (tpp) cc_final: 0.6509 (tpp) REVERT: H 592 ASP cc_start: 0.6715 (m-30) cc_final: 0.6333 (m-30) REVERT: H 593 PHE cc_start: 0.7945 (t80) cc_final: 0.7566 (t80) outliers start: 53 outliers final: 29 residues processed: 662 average time/residue: 0.1427 time to fit residues: 136.2771 Evaluate side-chains 640 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 609 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain H residue 502 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 61 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 169 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 ASN D 493 ASN ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 ASN H 302 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123869 restraints weight = 26426.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128428 restraints weight = 13305.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131430 restraints weight = 8067.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.133374 restraints weight = 5492.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134841 restraints weight = 4086.161| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17320 Z= 0.147 Angle : 0.593 7.814 23497 Z= 0.313 Chirality : 0.044 0.228 2603 Planarity : 0.004 0.042 2976 Dihedral : 6.682 118.885 2856 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.16 % Allowed : 16.09 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.30 (0.18), residues: 1978 helix: 1.29 (0.31), residues: 295 sheet: 0.63 (0.21), residues: 568 loop : -0.28 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 363 TYR 0.020 0.002 TYR H 553 PHE 0.017 0.002 PHE H 347 TRP 0.022 0.002 TRP A 361 HIS 0.012 0.001 HIS H 302 Details of bonding type rmsd covalent geometry : bond 0.00318 (17259) covalent geometry : angle 0.57271 (23366) SS BOND : bond 0.00182 ( 16) SS BOND : angle 1.65898 ( 32) hydrogen bonds : bond 0.04196 ( 560) hydrogen bonds : angle 5.28676 ( 1413) metal coordination : bond 0.01652 ( 12) link_BETA1-4 : bond 0.00499 ( 11) link_BETA1-4 : angle 1.72497 ( 33) link_BETA1-6 : bond 0.00338 ( 4) link_BETA1-6 : angle 1.64870 ( 12) link_NAG-ASN : bond 0.00282 ( 18) link_NAG-ASN : angle 2.60598 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 623 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 TRP cc_start: 0.8759 (m100) cc_final: 0.8531 (m100) REVERT: A 90 ASN cc_start: 0.7689 (p0) cc_final: 0.7448 (p0) REVERT: A 113 TYR cc_start: 0.7568 (t80) cc_final: 0.7355 (t80) REVERT: A 121 ILE cc_start: 0.7896 (tt) cc_final: 0.7341 (pt) REVERT: A 130 SER cc_start: 0.7377 (t) cc_final: 0.6606 (t) REVERT: A 154 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6719 (mt-10) REVERT: A 156 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6529 (mm-30) REVERT: A 163 PHE cc_start: 0.8308 (m-80) cc_final: 0.7861 (m-10) REVERT: A 293 ASP cc_start: 0.6453 (p0) cc_final: 0.5920 (p0) REVERT: A 315 MET cc_start: 0.6412 (mmm) cc_final: 0.5771 (mmm) REVERT: A 375 VAL cc_start: 0.8102 (t) cc_final: 0.7744 (p) REVERT: A 428 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6435 (mt-10) REVERT: A 443 GLN cc_start: 0.7727 (mp10) cc_final: 0.7372 (mp10) REVERT: A 447 ASN cc_start: 0.7722 (m-40) cc_final: 0.7465 (m-40) REVERT: A 458 ARG cc_start: 0.8094 (mtm110) cc_final: 0.7725 (ttp80) REVERT: A 471 LEU cc_start: 0.8438 (tp) cc_final: 0.8204 (tp) REVERT: A 502 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6583 (mt-10) REVERT: A 527 PHE cc_start: 0.7882 (p90) cc_final: 0.7388 (p90) REVERT: A 583 LYS cc_start: 0.7881 (tptt) cc_final: 0.7505 (tptt) REVERT: A 585 ASP cc_start: 0.6516 (t0) cc_final: 0.6181 (t0) REVERT: D 45 GLU cc_start: 0.7776 (tt0) cc_final: 0.7293 (tt0) REVERT: D 85 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.7123 (t0) REVERT: D 101 MET cc_start: 0.7080 (mmm) cc_final: 0.6507 (mmm) REVERT: D 105 LYS cc_start: 0.8107 (mttt) cc_final: 0.7685 (mtmt) REVERT: D 123 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6407 (mm-40) REVERT: D 125 PHE cc_start: 0.7228 (m-10) cc_final: 0.6441 (m-10) REVERT: D 135 GLN cc_start: 0.7306 (mm-40) cc_final: 0.7036 (mm-40) REVERT: D 141 ILE cc_start: 0.7888 (mt) cc_final: 0.7494 (mm) REVERT: D 142 SER cc_start: 0.8093 (t) cc_final: 0.7319 (p) REVERT: D 163 PHE cc_start: 0.7079 (m-80) cc_final: 0.6349 (m-80) REVERT: D 212 MET cc_start: 0.6227 (mmm) cc_final: 0.5770 (mmm) REVERT: D 244 ASP cc_start: 0.7097 (t70) cc_final: 0.6463 (t70) REVERT: D 252 ARG cc_start: 0.7506 (mtp180) cc_final: 0.6650 (mtp180) REVERT: D 270 THR cc_start: 0.7312 (p) cc_final: 0.7061 (t) REVERT: D 285 ASP cc_start: 0.5724 (p0) cc_final: 0.5383 (p0) REVERT: D 287 THR cc_start: 0.7412 (t) cc_final: 0.6828 (m) REVERT: D 330 LEU cc_start: 0.7599 (mt) cc_final: 0.7061 (mt) REVERT: D 356 ASP cc_start: 0.6703 (m-30) cc_final: 0.6178 (m-30) REVERT: D 362 VAL cc_start: 0.7871 (t) cc_final: 0.7571 (p) REVERT: D 363 ARG cc_start: 0.7863 (ttm110) cc_final: 0.7655 (ttm170) REVERT: D 393 VAL cc_start: 0.8008 (t) cc_final: 0.7688 (p) REVERT: D 396 LYS cc_start: 0.7757 (mttt) cc_final: 0.7419 (mttt) REVERT: D 405 PHE cc_start: 0.7659 (m-10) cc_final: 0.7287 (m-80) REVERT: D 428 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6544 (mt-10) REVERT: D 441 PHE cc_start: 0.8509 (t80) cc_final: 0.7782 (t80) REVERT: D 445 LEU cc_start: 0.8271 (tp) cc_final: 0.8005 (mt) REVERT: D 446 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6750 (mt-10) REVERT: D 453 LYS cc_start: 0.6923 (pttt) cc_final: 0.6520 (pttt) REVERT: D 460 TYR cc_start: 0.8324 (m-80) cc_final: 0.8093 (m-10) REVERT: D 465 TYR cc_start: 0.7687 (m-80) cc_final: 0.7099 (m-80) REVERT: D 474 ASN cc_start: 0.6209 (p0) cc_final: 0.5956 (p0) REVERT: D 486 PHE cc_start: 0.7889 (t80) cc_final: 0.7477 (t80) REVERT: D 487 HIS cc_start: 0.7727 (p-80) cc_final: 0.7434 (p-80) REVERT: D 512 ASP cc_start: 0.7103 (t0) cc_final: 0.6836 (t0) REVERT: D 546 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7574 (ttm-80) REVERT: D 573 HIS cc_start: 0.7312 (m170) cc_final: 0.6387 (m170) REVERT: D 577 LYS cc_start: 0.7634 (mmtt) cc_final: 0.7331 (mmtt) REVERT: E 74 ARG cc_start: 0.7409 (mtt-85) cc_final: 0.7163 (mtt-85) REVERT: E 76 THR cc_start: 0.7667 (m) cc_final: 0.7465 (p) REVERT: E 100 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7016 (tm-30) REVERT: E 111 LYS cc_start: 0.7865 (pttt) cc_final: 0.7596 (ptmt) REVERT: E 128 CYS cc_start: 0.4771 (OUTLIER) cc_final: 0.4568 (m) REVERT: E 131 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6635 (mt-10) REVERT: E 135 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7521 (mm110) REVERT: E 136 HIS cc_start: 0.7369 (m-70) cc_final: 0.6932 (m-70) REVERT: E 143 ILE cc_start: 0.8548 (mm) cc_final: 0.8276 (tp) REVERT: E 215 GLN cc_start: 0.7459 (mt0) cc_final: 0.7117 (mt0) REVERT: E 224 SER cc_start: 0.6998 (m) cc_final: 0.6507 (p) REVERT: E 234 GLU cc_start: 0.7374 (mp0) cc_final: 0.7101 (mp0) REVERT: E 241 GLN cc_start: 0.8076 (pp30) cc_final: 0.7802 (pp30) REVERT: E 251 GLU cc_start: 0.7361 (tp30) cc_final: 0.6701 (tp30) REVERT: E 256 MET cc_start: 0.7162 (ttp) cc_final: 0.6796 (ttp) REVERT: E 299 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6215 (mt-10) REVERT: E 303 THR cc_start: 0.8382 (m) cc_final: 0.7678 (t) REVERT: E 304 LEU cc_start: 0.8048 (mt) cc_final: 0.7822 (mt) REVERT: E 315 MET cc_start: 0.7189 (mmm) cc_final: 0.6947 (mmm) REVERT: E 320 SER cc_start: 0.8318 (p) cc_final: 0.7900 (t) REVERT: E 326 GLU cc_start: 0.6313 (mt-10) cc_final: 0.6023 (mt-10) REVERT: E 356 ASP cc_start: 0.6920 (m-30) cc_final: 0.6608 (m-30) REVERT: E 400 LYS cc_start: 0.7930 (pttt) cc_final: 0.7719 (ptpp) REVERT: E 409 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7579 (ttpp) REVERT: E 412 PRO cc_start: 0.8711 (Cg_endo) cc_final: 0.8263 (Cg_exo) REVERT: E 474 ASN cc_start: 0.7939 (m-40) cc_final: 0.7737 (m-40) REVERT: E 486 PHE cc_start: 0.7986 (t80) cc_final: 0.7585 (t80) REVERT: E 518 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7837 (mtp-110) REVERT: E 521 MET cc_start: 0.7191 (mtp) cc_final: 0.6677 (mtp) REVERT: E 525 MET cc_start: 0.7327 (mmt) cc_final: 0.6912 (mmt) REVERT: E 530 SER cc_start: 0.8307 (t) cc_final: 0.7713 (p) REVERT: E 546 ARG cc_start: 0.7833 (ttm170) cc_final: 0.7518 (ttm-80) REVERT: E 577 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7655 (mtpp) REVERT: E 588 ILE cc_start: 0.8422 (mt) cc_final: 0.7916 (tt) REVERT: H 74 ARG cc_start: 0.7103 (mtt90) cc_final: 0.6688 (mtt-85) REVERT: H 76 THR cc_start: 0.7714 (m) cc_final: 0.7348 (p) REVERT: H 100 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7031 (mm-30) REVERT: H 102 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7794 (m-10) REVERT: H 111 LYS cc_start: 0.7852 (pttt) cc_final: 0.7359 (pttt) REVERT: H 130 SER cc_start: 0.8472 (t) cc_final: 0.8000 (p) REVERT: H 154 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6546 (mt-10) REVERT: H 173 ASP cc_start: 0.7486 (m-30) cc_final: 0.7216 (m-30) REVERT: H 207 ASP cc_start: 0.6561 (t0) cc_final: 0.6310 (t0) REVERT: H 209 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6892 (mt-10) REVERT: H 228 ILE cc_start: 0.8400 (mp) cc_final: 0.8149 (mp) REVERT: H 241 GLN cc_start: 0.8103 (pp30) cc_final: 0.7782 (pp30) REVERT: H 249 ASP cc_start: 0.6967 (m-30) cc_final: 0.6450 (m-30) REVERT: H 252 ARG cc_start: 0.7464 (ttm170) cc_final: 0.7176 (mtm-85) REVERT: H 256 MET cc_start: 0.7511 (ttp) cc_final: 0.6999 (ttp) REVERT: H 275 ASN cc_start: 0.7492 (p0) cc_final: 0.7237 (p0) REVERT: H 301 ASP cc_start: 0.7412 (p0) cc_final: 0.7120 (p0) REVERT: H 303 THR cc_start: 0.8200 (m) cc_final: 0.7610 (t) REVERT: H 315 MET cc_start: 0.7284 (mmm) cc_final: 0.6881 (mmm) REVERT: H 330 LEU cc_start: 0.8229 (tp) cc_final: 0.7752 (tt) REVERT: H 341 GLN cc_start: 0.7980 (tt0) cc_final: 0.7455 (tm-30) REVERT: H 364 ARG cc_start: 0.7822 (ptp-170) cc_final: 0.7340 (ptm160) REVERT: H 381 GLN cc_start: 0.7357 (tp40) cc_final: 0.6806 (mm-40) REVERT: H 394 VAL cc_start: 0.8487 (t) cc_final: 0.8199 (m) REVERT: H 397 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6282 (mm-30) REVERT: H 404 LEU cc_start: 0.8458 (mp) cc_final: 0.8069 (mt) REVERT: H 455 GLN cc_start: 0.7887 (pm20) cc_final: 0.7669 (pm20) REVERT: H 463 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6982 (mt-10) REVERT: H 471 LEU cc_start: 0.8077 (tp) cc_final: 0.7736 (tp) REVERT: H 521 MET cc_start: 0.7464 (mtp) cc_final: 0.6888 (mtp) REVERT: H 546 ARG cc_start: 0.8095 (ttp80) cc_final: 0.7569 (ttp80) REVERT: H 592 ASP cc_start: 0.6730 (m-30) cc_final: 0.6233 (m-30) REVERT: H 593 PHE cc_start: 0.7967 (t80) cc_final: 0.7603 (t80) outliers start: 57 outliers final: 32 residues processed: 648 average time/residue: 0.1349 time to fit residues: 127.3926 Evaluate side-chains 647 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 610 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 128 CYS Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 502 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 90 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 ASN D 302 HIS ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 GLN H 136 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120896 restraints weight = 26502.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125360 restraints weight = 13507.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.128366 restraints weight = 8315.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.130388 restraints weight = 5736.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131669 restraints weight = 4264.976| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17320 Z= 0.259 Angle : 0.664 9.796 23497 Z= 0.351 Chirality : 0.047 0.232 2603 Planarity : 0.004 0.047 2976 Dihedral : 6.715 116.075 2856 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.05 % Allowed : 16.76 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.02 (0.18), residues: 1978 helix: 1.24 (0.30), residues: 285 sheet: 0.34 (0.21), residues: 599 loop : -0.51 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 252 TYR 0.027 0.002 TYR H 553 PHE 0.025 0.002 PHE D 314 TRP 0.024 0.003 TRP H 75 HIS 0.009 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00550 (17259) covalent geometry : angle 0.64410 (23366) SS BOND : bond 0.00410 ( 16) SS BOND : angle 1.65166 ( 32) hydrogen bonds : bond 0.05084 ( 560) hydrogen bonds : angle 5.39702 ( 1413) metal coordination : bond 0.01922 ( 12) link_BETA1-4 : bond 0.00528 ( 11) link_BETA1-4 : angle 1.84505 ( 33) link_BETA1-6 : bond 0.00337 ( 4) link_BETA1-6 : angle 1.75520 ( 12) link_NAG-ASN : bond 0.00553 ( 18) link_NAG-ASN : angle 2.80624 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 636 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 SER cc_start: 0.7332 (t) cc_final: 0.6626 (t) REVERT: A 153 ILE cc_start: 0.8289 (mt) cc_final: 0.7770 (tp) REVERT: A 154 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6920 (mt-10) REVERT: A 156 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6506 (mm-30) REVERT: A 241 GLN cc_start: 0.8122 (pp30) cc_final: 0.7861 (pp30) REVERT: A 271 PHE cc_start: 0.8134 (m-10) cc_final: 0.7638 (m-10) REVERT: A 315 MET cc_start: 0.6310 (mmm) cc_final: 0.5644 (mmm) REVERT: A 372 ARG cc_start: 0.7181 (ttp-110) cc_final: 0.6571 (ptm-80) REVERT: A 375 VAL cc_start: 0.8102 (t) cc_final: 0.7708 (p) REVERT: A 376 LYS cc_start: 0.8107 (tttt) cc_final: 0.7638 (tttt) REVERT: A 396 LYS cc_start: 0.7873 (mttt) cc_final: 0.7397 (mttt) REVERT: A 428 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6477 (mt-10) REVERT: A 438 VAL cc_start: 0.8286 (t) cc_final: 0.7829 (p) REVERT: A 447 ASN cc_start: 0.7783 (m-40) cc_final: 0.7463 (m-40) REVERT: A 458 ARG cc_start: 0.8102 (mtm110) cc_final: 0.7803 (ttp80) REVERT: A 471 LEU cc_start: 0.8472 (tp) cc_final: 0.8269 (tt) REVERT: A 511 LEU cc_start: 0.8356 (tp) cc_final: 0.8046 (mm) REVERT: A 527 PHE cc_start: 0.7905 (p90) cc_final: 0.7366 (p90) REVERT: A 530 SER cc_start: 0.8376 (t) cc_final: 0.7955 (p) REVERT: A 583 LYS cc_start: 0.7807 (tptt) cc_final: 0.7494 (tptt) REVERT: A 585 ASP cc_start: 0.6634 (t0) cc_final: 0.6356 (t0) REVERT: D 45 GLU cc_start: 0.7890 (tt0) cc_final: 0.7380 (tt0) REVERT: D 79 ILE cc_start: 0.7740 (mp) cc_final: 0.7481 (mm) REVERT: D 85 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7227 (t0) REVERT: D 95 ILE cc_start: 0.7976 (mt) cc_final: 0.7760 (mm) REVERT: D 101 MET cc_start: 0.7163 (mmm) cc_final: 0.6528 (mmm) REVERT: D 105 LYS cc_start: 0.8113 (mttt) cc_final: 0.7652 (mtmt) REVERT: D 131 GLU cc_start: 0.5722 (mt-10) cc_final: 0.5323 (mt-10) REVERT: D 135 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7127 (mm-40) REVERT: D 141 ILE cc_start: 0.7823 (mt) cc_final: 0.7349 (mm) REVERT: D 142 SER cc_start: 0.8164 (t) cc_final: 0.7446 (p) REVERT: D 156 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6552 (mm-30) REVERT: D 163 PHE cc_start: 0.7159 (m-80) cc_final: 0.6288 (m-80) REVERT: D 212 MET cc_start: 0.6334 (mmm) cc_final: 0.6019 (mmm) REVERT: D 244 ASP cc_start: 0.7048 (t70) cc_final: 0.6419 (t70) REVERT: D 252 ARG cc_start: 0.7578 (mtp180) cc_final: 0.6664 (mtp180) REVERT: D 270 THR cc_start: 0.7423 (p) cc_final: 0.7148 (t) REVERT: D 287 THR cc_start: 0.7449 (t) cc_final: 0.6901 (m) REVERT: D 330 LEU cc_start: 0.7409 (mt) cc_final: 0.6853 (mt) REVERT: D 339 ARG cc_start: 0.6762 (mtt-85) cc_final: 0.6463 (mmt-90) REVERT: D 357 ARG cc_start: 0.7422 (ptm-80) cc_final: 0.7197 (ptm-80) REVERT: D 362 VAL cc_start: 0.7925 (t) cc_final: 0.7553 (p) REVERT: D 396 LYS cc_start: 0.7825 (mttt) cc_final: 0.7548 (mttt) REVERT: D 405 PHE cc_start: 0.7690 (m-10) cc_final: 0.7436 (m-10) REVERT: D 428 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6533 (mt-10) REVERT: D 441 PHE cc_start: 0.8575 (t80) cc_final: 0.8014 (t80) REVERT: D 445 LEU cc_start: 0.8364 (tp) cc_final: 0.8126 (mt) REVERT: D 453 LYS cc_start: 0.7205 (pttt) cc_final: 0.6895 (pttt) REVERT: D 460 TYR cc_start: 0.8362 (m-80) cc_final: 0.8123 (m-10) REVERT: D 474 ASN cc_start: 0.6463 (p0) cc_final: 0.6228 (p0) REVERT: D 487 HIS cc_start: 0.7908 (p-80) cc_final: 0.7548 (p-80) REVERT: D 512 ASP cc_start: 0.7223 (t0) cc_final: 0.6992 (t0) REVERT: D 546 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7323 (ptm160) REVERT: D 573 HIS cc_start: 0.7366 (m170) cc_final: 0.6585 (m170) REVERT: D 577 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7364 (mmtt) REVERT: E 74 ARG cc_start: 0.7426 (mtt-85) cc_final: 0.7207 (mtt-85) REVERT: E 111 LYS cc_start: 0.7949 (pttt) cc_final: 0.7688 (ptmt) REVERT: E 128 CYS cc_start: 0.4856 (OUTLIER) cc_final: 0.4646 (m) REVERT: E 131 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6627 (mt-10) REVERT: E 135 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7568 (mm110) REVERT: E 136 HIS cc_start: 0.7464 (m-70) cc_final: 0.6987 (m-70) REVERT: E 143 ILE cc_start: 0.8476 (mm) cc_final: 0.8219 (tp) REVERT: E 167 GLN cc_start: 0.6973 (pm20) cc_final: 0.6530 (pm20) REVERT: E 215 GLN cc_start: 0.7526 (mt0) cc_final: 0.7167 (mt0) REVERT: E 224 SER cc_start: 0.7265 (m) cc_final: 0.6813 (p) REVERT: E 234 GLU cc_start: 0.7509 (mp0) cc_final: 0.7236 (mp0) REVERT: E 241 GLN cc_start: 0.8156 (pp30) cc_final: 0.7780 (pp30) REVERT: E 251 GLU cc_start: 0.7329 (tp30) cc_final: 0.6643 (tp30) REVERT: E 256 MET cc_start: 0.7190 (ttp) cc_final: 0.6764 (ttp) REVERT: E 299 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6258 (mt-10) REVERT: E 303 THR cc_start: 0.8321 (m) cc_final: 0.7512 (t) REVERT: E 321 SER cc_start: 0.7398 (p) cc_final: 0.7140 (t) REVERT: E 326 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6280 (tt0) REVERT: E 330 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7690 (tp) REVERT: E 356 ASP cc_start: 0.6959 (m-30) cc_final: 0.6744 (m-30) REVERT: E 373 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7639 (ttpp) REVERT: E 400 LYS cc_start: 0.7964 (pttt) cc_final: 0.7615 (ptpp) REVERT: E 409 LYS cc_start: 0.8408 (mtpt) cc_final: 0.7793 (ttpp) REVERT: E 412 PRO cc_start: 0.8771 (Cg_endo) cc_final: 0.8450 (Cg_exo) REVERT: E 474 ASN cc_start: 0.8037 (m-40) cc_final: 0.7802 (m-40) REVERT: E 486 PHE cc_start: 0.8079 (t80) cc_final: 0.7674 (t80) REVERT: E 493 ASN cc_start: 0.8083 (m-40) cc_final: 0.7864 (m-40) REVERT: E 502 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6848 (mt-10) REVERT: E 518 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7883 (mtp-110) REVERT: E 521 MET cc_start: 0.7253 (mtp) cc_final: 0.6766 (mtp) REVERT: E 525 MET cc_start: 0.7343 (mmt) cc_final: 0.6897 (mmt) REVERT: E 527 PHE cc_start: 0.7131 (p90) cc_final: 0.6740 (p90) REVERT: E 530 SER cc_start: 0.8450 (t) cc_final: 0.7936 (p) REVERT: E 568 SER cc_start: 0.8080 (p) cc_final: 0.7827 (t) REVERT: E 577 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7714 (mtpp) REVERT: E 588 ILE cc_start: 0.8440 (mt) cc_final: 0.7950 (tt) REVERT: H 52 LEU cc_start: 0.7552 (mt) cc_final: 0.7344 (mt) REVERT: H 74 ARG cc_start: 0.7200 (mtt90) cc_final: 0.6654 (mtt-85) REVERT: H 76 THR cc_start: 0.7641 (m) cc_final: 0.7277 (p) REVERT: H 81 TYR cc_start: 0.7969 (p90) cc_final: 0.7299 (p90) REVERT: H 100 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7108 (mm-30) REVERT: H 102 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7740 (m-10) REVERT: H 105 LYS cc_start: 0.8207 (mttm) cc_final: 0.7669 (mttm) REVERT: H 111 LYS cc_start: 0.7881 (pttt) cc_final: 0.7179 (pttt) REVERT: H 154 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6602 (mt-10) REVERT: H 173 ASP cc_start: 0.7497 (m-30) cc_final: 0.7253 (m-30) REVERT: H 215 GLN cc_start: 0.7545 (mt0) cc_final: 0.7168 (mt0) REVERT: H 228 ILE cc_start: 0.8381 (mp) cc_final: 0.8169 (mp) REVERT: H 241 GLN cc_start: 0.8113 (pp30) cc_final: 0.7811 (pp30) REVERT: H 249 ASP cc_start: 0.6965 (m-30) cc_final: 0.6545 (m-30) REVERT: H 256 MET cc_start: 0.7560 (ttp) cc_final: 0.6778 (ttp) REVERT: H 267 ASP cc_start: 0.7279 (t0) cc_final: 0.6731 (t0) REVERT: H 271 PHE cc_start: 0.8193 (m-80) cc_final: 0.7809 (m-80) REVERT: H 275 ASN cc_start: 0.7507 (p0) cc_final: 0.7189 (p0) REVERT: H 303 THR cc_start: 0.8200 (m) cc_final: 0.7428 (t) REVERT: H 314 PHE cc_start: 0.8502 (p90) cc_final: 0.8048 (p90) REVERT: H 315 MET cc_start: 0.7267 (mmm) cc_final: 0.6793 (mmm) REVERT: H 330 LEU cc_start: 0.8218 (tp) cc_final: 0.7776 (tt) REVERT: H 341 GLN cc_start: 0.8114 (tt0) cc_final: 0.7590 (tm-30) REVERT: H 364 ARG cc_start: 0.7913 (ptp-170) cc_final: 0.7454 (ptm160) REVERT: H 372 ARG cc_start: 0.7501 (mtp-110) cc_final: 0.7175 (mtm-85) REVERT: H 381 GLN cc_start: 0.7394 (tp40) cc_final: 0.6813 (mm-40) REVERT: H 394 VAL cc_start: 0.8649 (t) cc_final: 0.8354 (m) REVERT: H 397 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6333 (mm-30) REVERT: H 404 LEU cc_start: 0.8506 (mp) cc_final: 0.8132 (mt) REVERT: H 463 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7171 (mt-10) REVERT: H 471 LEU cc_start: 0.8138 (tp) cc_final: 0.7851 (tp) REVERT: H 593 PHE cc_start: 0.7911 (t80) cc_final: 0.7596 (t80) REVERT: H 594 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6483 (mm-30) outliers start: 73 outliers final: 46 residues processed: 669 average time/residue: 0.1351 time to fit residues: 131.0928 Evaluate side-chains 661 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 611 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain E residue 128 CYS Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 399 GLN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 563 ILE Chi-restraints excluded: chain H residue 572 SER Chi-restraints excluded: chain H residue 591 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN D 86 ASN D 302 HIS D 493 ASN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN E 291 HIS H 136 HIS H 302 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126089 restraints weight = 26256.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130577 restraints weight = 13337.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.133566 restraints weight = 8183.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135483 restraints weight = 5640.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136854 restraints weight = 4247.589| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17320 Z= 0.120 Angle : 0.591 11.133 23497 Z= 0.307 Chirality : 0.044 0.218 2603 Planarity : 0.003 0.044 2976 Dihedral : 6.277 113.317 2856 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.33 % Allowed : 19.26 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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 (0.18), residues: 1978 helix: 1.37 (0.31), residues: 293 sheet: 0.53 (0.22), residues: 558 loop : -0.40 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 252 TYR 0.033 0.001 TYR D 119 PHE 0.030 0.002 PHE D 486 TRP 0.024 0.002 TRP A 361 HIS 0.008 0.001 HIS H 189 Details of bonding type rmsd covalent geometry : bond 0.00261 (17259) covalent geometry : angle 0.57344 (23366) SS BOND : bond 0.00233 ( 16) SS BOND : angle 1.38966 ( 32) hydrogen bonds : bond 0.03808 ( 560) hydrogen bonds : angle 5.29800 ( 1413) metal coordination : bond 0.00773 ( 12) link_BETA1-4 : bond 0.00483 ( 11) link_BETA1-4 : angle 1.70806 ( 33) link_BETA1-6 : bond 0.00509 ( 4) link_BETA1-6 : angle 1.63370 ( 12) link_NAG-ASN : bond 0.00207 ( 18) link_NAG-ASN : angle 2.45287 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 639 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.7626 (p0) cc_final: 0.7419 (p0) REVERT: A 97 TYR cc_start: 0.6836 (t80) cc_final: 0.6635 (t80) REVERT: A 121 ILE cc_start: 0.7923 (tt) cc_final: 0.7302 (pt) REVERT: A 153 ILE cc_start: 0.8175 (mt) cc_final: 0.7653 (tp) REVERT: A 154 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6733 (mt-10) REVERT: A 156 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6465 (mm-30) REVERT: A 271 PHE cc_start: 0.8086 (m-10) cc_final: 0.7646 (m-10) REVERT: A 315 MET cc_start: 0.6268 (mmm) cc_final: 0.5723 (mmm) REVERT: A 339 ARG cc_start: 0.7423 (mmm-85) cc_final: 0.7004 (mmm-85) REVERT: A 375 VAL cc_start: 0.8142 (t) cc_final: 0.7718 (p) REVERT: A 396 LYS cc_start: 0.7884 (mttt) cc_final: 0.7375 (mttt) REVERT: A 428 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6466 (mt-10) REVERT: A 447 ASN cc_start: 0.7756 (m-40) cc_final: 0.7510 (m-40) REVERT: A 458 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7829 (ttp80) REVERT: A 471 LEU cc_start: 0.8472 (tp) cc_final: 0.8266 (tp) REVERT: A 521 MET cc_start: 0.7111 (mtp) cc_final: 0.6900 (mtp) REVERT: A 527 PHE cc_start: 0.7799 (p90) cc_final: 0.7241 (p90) REVERT: A 583 LYS cc_start: 0.7799 (tptt) cc_final: 0.7450 (tptt) REVERT: A 585 ASP cc_start: 0.6599 (t0) cc_final: 0.6247 (t0) REVERT: D 45 GLU cc_start: 0.7888 (tt0) cc_final: 0.7348 (tt0) REVERT: D 59 ILE cc_start: 0.7654 (mt) cc_final: 0.7321 (mt) REVERT: D 79 ILE cc_start: 0.7737 (mp) cc_final: 0.7460 (mm) REVERT: D 85 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7203 (t0) REVERT: D 101 MET cc_start: 0.7160 (mmm) cc_final: 0.6472 (mmm) REVERT: D 105 LYS cc_start: 0.8046 (mttt) cc_final: 0.7562 (mtmt) REVERT: D 141 ILE cc_start: 0.7767 (mt) cc_final: 0.7347 (mm) REVERT: D 142 SER cc_start: 0.8118 (t) cc_final: 0.7298 (p) REVERT: D 156 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6502 (mm-30) REVERT: D 163 PHE cc_start: 0.7067 (m-80) cc_final: 0.6810 (m-80) REVERT: D 212 MET cc_start: 0.6233 (mmm) cc_final: 0.5844 (mmm) REVERT: D 244 ASP cc_start: 0.7020 (t70) cc_final: 0.6247 (t70) REVERT: D 270 THR cc_start: 0.7322 (p) cc_final: 0.7037 (t) REVERT: D 287 THR cc_start: 0.7389 (t) cc_final: 0.7043 (m) REVERT: D 330 LEU cc_start: 0.7580 (mt) cc_final: 0.6974 (mt) REVERT: D 339 ARG cc_start: 0.6702 (mtt-85) cc_final: 0.6470 (mmt-90) REVERT: D 362 VAL cc_start: 0.7902 (t) cc_final: 0.7681 (p) REVERT: D 374 LEU cc_start: 0.8462 (mt) cc_final: 0.8239 (mt) REVERT: D 404 LEU cc_start: 0.7775 (mp) cc_final: 0.7482 (mt) REVERT: D 405 PHE cc_start: 0.7643 (m-10) cc_final: 0.7291 (m-80) REVERT: D 428 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6524 (mt-10) REVERT: D 445 LEU cc_start: 0.8294 (tp) cc_final: 0.8068 (mt) REVERT: D 453 LYS cc_start: 0.7084 (pttt) cc_final: 0.6788 (pttt) REVERT: D 474 ASN cc_start: 0.6460 (p0) cc_final: 0.6165 (p0) REVERT: D 487 HIS cc_start: 0.7824 (p-80) cc_final: 0.7503 (p-80) REVERT: D 512 ASP cc_start: 0.7201 (t0) cc_final: 0.6897 (t0) REVERT: D 546 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7661 (ttm-80) REVERT: D 573 HIS cc_start: 0.7219 (m170) cc_final: 0.6677 (m170) REVERT: D 577 LYS cc_start: 0.7717 (mmtt) cc_final: 0.7341 (mmtt) REVERT: D 588 ILE cc_start: 0.8654 (mt) cc_final: 0.8363 (mm) REVERT: E 48 LEU cc_start: 0.8464 (tp) cc_final: 0.8263 (tt) REVERT: E 74 ARG cc_start: 0.7406 (mtt-85) cc_final: 0.7193 (mtt-85) REVERT: E 76 THR cc_start: 0.7622 (m) cc_final: 0.7387 (p) REVERT: E 100 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: E 102 PHE cc_start: 0.7809 (m-80) cc_final: 0.7571 (m-80) REVERT: E 111 LYS cc_start: 0.7894 (pttt) cc_final: 0.7687 (ptmt) REVERT: E 131 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6520 (mt-10) REVERT: E 135 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7469 (mm110) REVERT: E 136 HIS cc_start: 0.7433 (m-70) cc_final: 0.6970 (m-70) REVERT: E 143 ILE cc_start: 0.8467 (mm) cc_final: 0.8144 (tp) REVERT: E 167 GLN cc_start: 0.6818 (pm20) cc_final: 0.6408 (pm20) REVERT: E 215 GLN cc_start: 0.7533 (mt0) cc_final: 0.7151 (mt0) REVERT: E 224 SER cc_start: 0.7275 (m) cc_final: 0.6821 (p) REVERT: E 234 GLU cc_start: 0.7476 (mp0) cc_final: 0.7216 (mp0) REVERT: E 241 GLN cc_start: 0.8220 (pp30) cc_final: 0.7844 (pp30) REVERT: E 251 GLU cc_start: 0.7246 (tp30) cc_final: 0.6463 (tp30) REVERT: E 256 MET cc_start: 0.7191 (ttp) cc_final: 0.6758 (ttp) REVERT: E 299 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6182 (mt-10) REVERT: E 301 ASP cc_start: 0.7760 (p0) cc_final: 0.7188 (t0) REVERT: E 303 THR cc_start: 0.8396 (m) cc_final: 0.7571 (t) REVERT: E 315 MET cc_start: 0.7025 (mmm) cc_final: 0.6272 (mmm) REVERT: E 321 SER cc_start: 0.7458 (p) cc_final: 0.7162 (t) REVERT: E 326 GLU cc_start: 0.6507 (mt-10) cc_final: 0.6227 (tt0) REVERT: E 356 ASP cc_start: 0.6925 (m-30) cc_final: 0.6606 (m-30) REVERT: E 396 LYS cc_start: 0.7328 (mttt) cc_final: 0.6952 (mtmt) REVERT: E 400 LYS cc_start: 0.7980 (pttt) cc_final: 0.7699 (ptpp) REVERT: E 409 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7487 (ttpt) REVERT: E 412 PRO cc_start: 0.8709 (Cg_endo) cc_final: 0.8349 (Cg_exo) REVERT: E 474 ASN cc_start: 0.7991 (m-40) cc_final: 0.7736 (m-40) REVERT: E 486 PHE cc_start: 0.8014 (t80) cc_final: 0.7577 (t80) REVERT: E 493 ASN cc_start: 0.7858 (m-40) cc_final: 0.7562 (m110) REVERT: E 502 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6853 (mt-10) REVERT: E 518 ARG cc_start: 0.8194 (ttp-110) cc_final: 0.7822 (mtp-110) REVERT: E 521 MET cc_start: 0.7249 (mtp) cc_final: 0.6738 (mtp) REVERT: E 525 MET cc_start: 0.7328 (mmt) cc_final: 0.6892 (mmt) REVERT: E 527 PHE cc_start: 0.7034 (p90) cc_final: 0.6696 (p90) REVERT: E 530 SER cc_start: 0.8442 (t) cc_final: 0.7901 (p) REVERT: E 546 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7587 (ttm-80) REVERT: E 577 LYS cc_start: 0.8012 (mtpp) cc_final: 0.7700 (mtpp) REVERT: E 588 ILE cc_start: 0.8400 (mt) cc_final: 0.7921 (tt) REVERT: H 52 LEU cc_start: 0.7495 (mt) cc_final: 0.7293 (mt) REVERT: H 74 ARG cc_start: 0.7162 (mtt90) cc_final: 0.6686 (mtt-85) REVERT: H 76 THR cc_start: 0.7649 (m) cc_final: 0.7289 (p) REVERT: H 100 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6783 (mm-30) REVERT: H 102 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7733 (m-10) REVERT: H 111 LYS cc_start: 0.7848 (pttt) cc_final: 0.7374 (pttt) REVERT: H 124 GLN cc_start: 0.7184 (tm-30) cc_final: 0.6533 (tm-30) REVERT: H 130 SER cc_start: 0.8578 (t) cc_final: 0.7991 (p) REVERT: H 173 ASP cc_start: 0.7474 (m-30) cc_final: 0.7206 (m-30) REVERT: H 215 GLN cc_start: 0.7546 (mt0) cc_final: 0.7146 (mt0) REVERT: H 217 PHE cc_start: 0.8309 (m-80) cc_final: 0.7805 (m-80) REVERT: H 228 ILE cc_start: 0.8352 (mp) cc_final: 0.7975 (mm) REVERT: H 241 GLN cc_start: 0.8166 (pp30) cc_final: 0.7870 (pp30) REVERT: H 249 ASP cc_start: 0.6960 (m-30) cc_final: 0.6522 (m-30) REVERT: H 252 ARG cc_start: 0.7352 (ttm170) cc_final: 0.7043 (mtm-85) REVERT: H 256 MET cc_start: 0.7546 (ttp) cc_final: 0.6800 (ttp) REVERT: H 267 ASP cc_start: 0.7275 (t0) cc_final: 0.6782 (t0) REVERT: H 271 PHE cc_start: 0.8075 (m-80) cc_final: 0.7724 (m-80) REVERT: H 275 ASN cc_start: 0.7478 (p0) cc_final: 0.7236 (p0) REVERT: H 303 THR cc_start: 0.8342 (m) cc_final: 0.7519 (t) REVERT: H 314 PHE cc_start: 0.8475 (p90) cc_final: 0.8014 (p90) REVERT: H 315 MET cc_start: 0.7224 (mmm) cc_final: 0.6823 (mmm) REVERT: H 330 LEU cc_start: 0.8249 (tp) cc_final: 0.7817 (tt) REVERT: H 341 GLN cc_start: 0.8028 (tt0) cc_final: 0.7550 (tm-30) REVERT: H 364 ARG cc_start: 0.7833 (ptp-170) cc_final: 0.7373 (ptm160) REVERT: H 372 ARG cc_start: 0.7530 (mtp-110) cc_final: 0.7192 (mtm-85) REVERT: H 381 GLN cc_start: 0.7282 (tp40) cc_final: 0.6747 (mm-40) REVERT: H 394 VAL cc_start: 0.8620 (t) cc_final: 0.8306 (m) REVERT: H 397 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6254 (mm-30) REVERT: H 404 LEU cc_start: 0.8533 (mp) cc_final: 0.8167 (mt) REVERT: H 463 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7142 (mt-10) REVERT: H 521 MET cc_start: 0.7433 (mtp) cc_final: 0.6878 (mtp) REVERT: H 543 ILE cc_start: 0.7841 (mt) cc_final: 0.7625 (mt) REVERT: H 593 PHE cc_start: 0.7975 (t80) cc_final: 0.7729 (t80) outliers start: 60 outliers final: 42 residues processed: 664 average time/residue: 0.1378 time to fit residues: 132.8134 Evaluate side-chains 647 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 602 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 399 GLN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 502 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 161 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 109 optimal weight: 0.2980 chunk 163 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 HIS A 302 HIS ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 188 GLN D 302 HIS D 493 ASN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 HIS E 598 HIS H 136 HIS H 177 ASN H 189 HIS H 190 ASN H 345 GLN H 392 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118784 restraints weight = 26251.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123209 restraints weight = 13248.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126161 restraints weight = 8116.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128131 restraints weight = 5587.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129516 restraints weight = 4166.062| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 17320 Z= 0.312 Angle : 0.716 10.436 23497 Z= 0.376 Chirality : 0.049 0.231 2603 Planarity : 0.004 0.056 2976 Dihedral : 6.643 111.604 2856 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.77 % Allowed : 20.20 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.27 (0.18), residues: 1978 helix: 0.99 (0.30), residues: 285 sheet: 0.22 (0.21), residues: 598 loop : -0.70 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 549 TYR 0.030 0.003 TYR E 113 PHE 0.031 0.003 PHE E 55 TRP 0.031 0.003 TRP A 361 HIS 0.012 0.002 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00660 (17259) covalent geometry : angle 0.69686 (23366) SS BOND : bond 0.00365 ( 16) SS BOND : angle 1.70456 ( 32) hydrogen bonds : bond 0.05419 ( 560) hydrogen bonds : angle 5.54348 ( 1413) metal coordination : bond 0.02085 ( 12) link_BETA1-4 : bond 0.00487 ( 11) link_BETA1-4 : angle 1.88790 ( 33) link_BETA1-6 : bond 0.00308 ( 4) link_BETA1-6 : angle 1.82901 ( 12) link_NAG-ASN : bond 0.00743 ( 18) link_NAG-ASN : angle 2.87996 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 652 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 121 ILE cc_start: 0.7983 (tt) cc_final: 0.7349 (pt) REVERT: A 130 SER cc_start: 0.7324 (t) cc_final: 0.6625 (t) REVERT: A 153 ILE cc_start: 0.8223 (mt) cc_final: 0.7713 (tp) REVERT: A 154 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6886 (mt-10) REVERT: A 156 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6312 (mm-30) REVERT: A 215 GLN cc_start: 0.7190 (tm-30) cc_final: 0.6563 (tm-30) REVERT: A 241 GLN cc_start: 0.8233 (pp30) cc_final: 0.7992 (pp30) REVERT: A 315 MET cc_start: 0.6186 (mmm) cc_final: 0.5829 (mmm) REVERT: A 363 ARG cc_start: 0.8094 (ttm170) cc_final: 0.7789 (ttm170) REVERT: A 372 ARG cc_start: 0.7267 (ttp-110) cc_final: 0.6637 (ptm-80) REVERT: A 375 VAL cc_start: 0.8003 (t) cc_final: 0.7582 (m) REVERT: A 376 LYS cc_start: 0.8061 (tttt) cc_final: 0.7498 (tttt) REVERT: A 396 LYS cc_start: 0.7941 (mttt) cc_final: 0.7739 (mttt) REVERT: A 428 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6497 (mt-10) REVERT: A 438 VAL cc_start: 0.8294 (t) cc_final: 0.7847 (p) REVERT: A 447 ASN cc_start: 0.7825 (m-40) cc_final: 0.7547 (m-40) REVERT: A 458 ARG cc_start: 0.8134 (mtm110) cc_final: 0.7874 (ttp80) REVERT: A 469 VAL cc_start: 0.7650 (t) cc_final: 0.6825 (p) REVERT: A 471 LEU cc_start: 0.8483 (tp) cc_final: 0.8274 (tt) REVERT: A 492 GLU cc_start: 0.7070 (pt0) cc_final: 0.6823 (pt0) REVERT: A 527 PHE cc_start: 0.7871 (p90) cc_final: 0.7367 (p90) REVERT: A 530 SER cc_start: 0.8335 (t) cc_final: 0.7907 (p) REVERT: A 583 LYS cc_start: 0.7878 (tptt) cc_final: 0.7581 (tptt) REVERT: A 585 ASP cc_start: 0.6655 (t0) cc_final: 0.6358 (t0) REVERT: D 45 GLU cc_start: 0.7827 (tt0) cc_final: 0.7330 (tt0) REVERT: D 79 ILE cc_start: 0.7770 (mp) cc_final: 0.7542 (mm) REVERT: D 85 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7310 (t0) REVERT: D 95 ILE cc_start: 0.7969 (mt) cc_final: 0.7765 (mm) REVERT: D 101 MET cc_start: 0.7091 (mmm) cc_final: 0.6461 (mmm) REVERT: D 105 LYS cc_start: 0.8106 (mttt) cc_final: 0.7616 (mtmt) REVERT: D 135 GLN cc_start: 0.7171 (mm110) cc_final: 0.6858 (mm110) REVERT: D 141 ILE cc_start: 0.7748 (mt) cc_final: 0.7434 (mm) REVERT: D 142 SER cc_start: 0.8153 (t) cc_final: 0.7436 (p) REVERT: D 156 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6586 (mm-30) REVERT: D 163 PHE cc_start: 0.7207 (m-80) cc_final: 0.6195 (m-80) REVERT: D 212 MET cc_start: 0.6372 (mmm) cc_final: 0.6062 (mmm) REVERT: D 244 ASP cc_start: 0.7121 (t70) cc_final: 0.6425 (t70) REVERT: D 252 ARG cc_start: 0.7560 (mtp180) cc_final: 0.6722 (ttp-170) REVERT: D 270 THR cc_start: 0.7366 (p) cc_final: 0.7122 (t) REVERT: D 287 THR cc_start: 0.7435 (t) cc_final: 0.7021 (m) REVERT: D 330 LEU cc_start: 0.7567 (mt) cc_final: 0.7037 (mt) REVERT: D 339 ARG cc_start: 0.6963 (mtt180) cc_final: 0.6651 (mmt-90) REVERT: D 362 VAL cc_start: 0.8109 (t) cc_final: 0.7838 (p) REVERT: D 404 LEU cc_start: 0.7806 (mp) cc_final: 0.7552 (mt) REVERT: D 405 PHE cc_start: 0.7672 (m-10) cc_final: 0.7389 (m-10) REVERT: D 428 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6519 (mt-10) REVERT: D 441 PHE cc_start: 0.8577 (t80) cc_final: 0.7945 (t80) REVERT: D 445 LEU cc_start: 0.8364 (tp) cc_final: 0.8150 (mt) REVERT: D 453 LYS cc_start: 0.7339 (pttt) cc_final: 0.6781 (pttt) REVERT: D 455 GLN cc_start: 0.7817 (mp10) cc_final: 0.7366 (mp10) REVERT: D 474 ASN cc_start: 0.6647 (p0) cc_final: 0.6324 (p0) REVERT: D 483 ARG cc_start: 0.7382 (ttt90) cc_final: 0.7146 (ttt90) REVERT: D 487 HIS cc_start: 0.7907 (p-80) cc_final: 0.7559 (p-80) REVERT: D 492 GLU cc_start: 0.6907 (pt0) cc_final: 0.6663 (pt0) REVERT: D 509 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7304 (t) REVERT: D 512 ASP cc_start: 0.7252 (t0) cc_final: 0.7040 (t0) REVERT: D 544 TRP cc_start: 0.8169 (m100) cc_final: 0.7708 (m100) REVERT: D 546 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7691 (ttm-80) REVERT: D 573 HIS cc_start: 0.7508 (m170) cc_final: 0.6965 (m170) REVERT: D 577 LYS cc_start: 0.7794 (mmtt) cc_final: 0.7430 (mmtt) REVERT: E 74 ARG cc_start: 0.7427 (mtt-85) cc_final: 0.7160 (mtt-85) REVERT: E 76 THR cc_start: 0.7736 (m) cc_final: 0.7451 (p) REVERT: E 111 LYS cc_start: 0.8010 (pttt) cc_final: 0.7795 (ptmt) REVERT: E 131 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6463 (mt-10) REVERT: E 136 HIS cc_start: 0.7460 (m-70) cc_final: 0.6957 (m-70) REVERT: E 143 ILE cc_start: 0.8398 (mm) cc_final: 0.8119 (tp) REVERT: E 209 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7008 (mm-30) REVERT: E 215 GLN cc_start: 0.7536 (mt0) cc_final: 0.7140 (mt0) REVERT: E 224 SER cc_start: 0.7457 (m) cc_final: 0.7095 (p) REVERT: E 241 GLN cc_start: 0.8175 (pp30) cc_final: 0.7835 (pp30) REVERT: E 251 GLU cc_start: 0.7333 (tp30) cc_final: 0.6596 (tp30) REVERT: E 256 MET cc_start: 0.7199 (ttp) cc_final: 0.6794 (ttp) REVERT: E 299 GLU cc_start: 0.6684 (mt-10) cc_final: 0.6191 (mt-10) REVERT: E 303 THR cc_start: 0.8315 (m) cc_final: 0.7743 (t) REVERT: E 315 MET cc_start: 0.7119 (mmm) cc_final: 0.6493 (mmm) REVERT: E 321 SER cc_start: 0.7607 (p) cc_final: 0.7283 (t) REVERT: E 326 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6229 (tt0) REVERT: E 364 ARG cc_start: 0.7474 (mtm180) cc_final: 0.7233 (mtm180) REVERT: E 392 HIS cc_start: 0.8398 (m90) cc_final: 0.8052 (m-70) REVERT: E 400 LYS cc_start: 0.8042 (pttt) cc_final: 0.7635 (ptpp) REVERT: E 409 LYS cc_start: 0.8390 (mtpt) cc_final: 0.7881 (ttpp) REVERT: E 412 PRO cc_start: 0.8791 (Cg_endo) cc_final: 0.8524 (Cg_exo) REVERT: E 486 PHE cc_start: 0.8148 (t80) cc_final: 0.7764 (t80) REVERT: E 502 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6900 (mt-10) REVERT: E 518 ARG cc_start: 0.8277 (ttp-110) cc_final: 0.7557 (mtp85) REVERT: E 521 MET cc_start: 0.7250 (mtp) cc_final: 0.6748 (mtp) REVERT: E 525 MET cc_start: 0.7404 (mmt) cc_final: 0.6917 (mmm) REVERT: E 527 PHE cc_start: 0.7201 (p90) cc_final: 0.6797 (p90) REVERT: E 530 SER cc_start: 0.8512 (t) cc_final: 0.8036 (p) REVERT: E 568 SER cc_start: 0.8129 (p) cc_final: 0.7886 (t) REVERT: E 577 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7757 (mtpp) REVERT: E 588 ILE cc_start: 0.8423 (mt) cc_final: 0.7948 (tt) REVERT: H 52 LEU cc_start: 0.7623 (mt) cc_final: 0.7409 (mt) REVERT: H 74 ARG cc_start: 0.7174 (mtt90) cc_final: 0.6684 (mtt-85) REVERT: H 76 THR cc_start: 0.7642 (m) cc_final: 0.7279 (p) REVERT: H 100 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6934 (mm-30) REVERT: H 105 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7861 (ptpp) REVERT: H 111 LYS cc_start: 0.7905 (pttt) cc_final: 0.7450 (pttt) REVERT: H 124 GLN cc_start: 0.7296 (tm-30) cc_final: 0.6698 (tm-30) REVERT: H 173 ASP cc_start: 0.7462 (m-30) cc_final: 0.7232 (m-30) REVERT: H 215 GLN cc_start: 0.7555 (mt0) cc_final: 0.7168 (mt0) REVERT: H 217 PHE cc_start: 0.8289 (m-80) cc_final: 0.7810 (m-80) REVERT: H 228 ILE cc_start: 0.8368 (mp) cc_final: 0.8161 (mp) REVERT: H 241 GLN cc_start: 0.8178 (pp30) cc_final: 0.7899 (pp30) REVERT: H 249 ASP cc_start: 0.7054 (m-30) cc_final: 0.6626 (m-30) REVERT: H 256 MET cc_start: 0.7559 (ttp) cc_final: 0.6792 (ttp) REVERT: H 267 ASP cc_start: 0.7387 (t0) cc_final: 0.6764 (t0) REVERT: H 273 LYS cc_start: 0.7587 (tttt) cc_final: 0.7294 (tttt) REVERT: H 275 ASN cc_start: 0.7509 (p0) cc_final: 0.7221 (p0) REVERT: H 292 GLN cc_start: 0.7671 (tp40) cc_final: 0.7201 (tp40) REVERT: H 303 THR cc_start: 0.8224 (m) cc_final: 0.7427 (t) REVERT: H 314 PHE cc_start: 0.8541 (p90) cc_final: 0.8065 (p90) REVERT: H 315 MET cc_start: 0.7220 (mmm) cc_final: 0.6771 (mmm) REVERT: H 341 GLN cc_start: 0.8156 (tt0) cc_final: 0.7900 (tt0) REVERT: H 350 MET cc_start: 0.7958 (ptp) cc_final: 0.7730 (ptp) REVERT: H 362 VAL cc_start: 0.8398 (t) cc_final: 0.8099 (p) REVERT: H 364 ARG cc_start: 0.7963 (ptp-170) cc_final: 0.7168 (ptm160) REVERT: H 373 LYS cc_start: 0.8021 (ttpp) cc_final: 0.7320 (ttpp) REVERT: H 381 GLN cc_start: 0.7315 (tp40) cc_final: 0.6817 (mm-40) REVERT: H 394 VAL cc_start: 0.8679 (t) cc_final: 0.8377 (m) REVERT: H 397 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6298 (mm-30) REVERT: H 404 LEU cc_start: 0.8512 (mp) cc_final: 0.8142 (mt) REVERT: H 463 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7184 (mt-10) REVERT: H 521 MET cc_start: 0.7423 (mtp) cc_final: 0.6902 (mtp) REVERT: H 584 ASN cc_start: 0.7934 (t0) cc_final: 0.7589 (t0) REVERT: H 593 PHE cc_start: 0.7916 (t80) cc_final: 0.7468 (t80) REVERT: H 594 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6443 (mm-30) outliers start: 68 outliers final: 51 residues processed: 683 average time/residue: 0.1448 time to fit residues: 142.5537 Evaluate side-chains 700 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 646 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 214 TYR Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 399 GLN Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 474 ASN Chi-restraints excluded: chain H residue 572 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 117 optimal weight: 0.0870 chunk 146 optimal weight: 0.0070 chunk 158 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 50 optimal weight: 0.0670 chunk 177 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN A 302 HIS A 513 GLN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS D 302 HIS ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 ASN E 236 ASN E 487 HIS H 136 HIS H 177 ASN H 190 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.141963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123897 restraints weight = 26127.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128424 restraints weight = 13076.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.131411 restraints weight = 7932.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133401 restraints weight = 5412.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.134762 restraints weight = 3991.761| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17320 Z= 0.109 Angle : 0.603 12.668 23497 Z= 0.315 Chirality : 0.043 0.223 2603 Planarity : 0.004 0.045 2976 Dihedral : 6.093 109.707 2856 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.00 % Allowed : 22.03 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.09 (0.19), residues: 1978 helix: 1.31 (0.31), residues: 294 sheet: 0.48 (0.22), residues: 563 loop : -0.47 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 549 TYR 0.022 0.001 TYR H 553 PHE 0.028 0.001 PHE E 55 TRP 0.037 0.002 TRP D 179 HIS 0.006 0.001 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00236 (17259) covalent geometry : angle 0.58852 (23366) SS BOND : bond 0.00252 ( 16) SS BOND : angle 1.32387 ( 32) hydrogen bonds : bond 0.03592 ( 560) hydrogen bonds : angle 5.20220 ( 1413) metal coordination : bond 0.00385 ( 12) link_BETA1-4 : bond 0.00450 ( 11) link_BETA1-4 : angle 1.73232 ( 33) link_BETA1-6 : bond 0.00484 ( 4) link_BETA1-6 : angle 1.46784 ( 12) link_NAG-ASN : bond 0.00233 ( 18) link_NAG-ASN : angle 2.24905 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 620 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.7894 (tt) cc_final: 0.7289 (pt) REVERT: A 130 SER cc_start: 0.7177 (t) cc_final: 0.6441 (t) REVERT: A 153 ILE cc_start: 0.8057 (mt) cc_final: 0.7508 (tp) REVERT: A 154 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6775 (mt-10) REVERT: A 156 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6507 (mm-30) REVERT: A 339 ARG cc_start: 0.7448 (mmm-85) cc_final: 0.7153 (mmm-85) REVERT: A 340 LYS cc_start: 0.7437 (mttt) cc_final: 0.7204 (mttt) REVERT: A 375 VAL cc_start: 0.8113 (t) cc_final: 0.7780 (p) REVERT: A 396 LYS cc_start: 0.7921 (mttt) cc_final: 0.7575 (mttt) REVERT: A 428 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6490 (mt-10) REVERT: A 447 ASN cc_start: 0.7750 (m-40) cc_final: 0.7528 (m-40) REVERT: A 471 LEU cc_start: 0.8468 (tp) cc_final: 0.8264 (tp) REVERT: A 527 PHE cc_start: 0.7734 (p90) cc_final: 0.7127 (p90) REVERT: A 583 LYS cc_start: 0.7867 (tptt) cc_final: 0.7572 (tptt) REVERT: A 585 ASP cc_start: 0.6614 (t0) cc_final: 0.6245 (t0) REVERT: D 45 GLU cc_start: 0.7787 (tt0) cc_final: 0.7270 (tt0) REVERT: D 96 LEU cc_start: 0.8161 (mt) cc_final: 0.7827 (mp) REVERT: D 101 MET cc_start: 0.7141 (mmm) cc_final: 0.6421 (mmm) REVERT: D 105 LYS cc_start: 0.7954 (mttt) cc_final: 0.7440 (mtmt) REVERT: D 135 GLN cc_start: 0.7251 (mm110) cc_final: 0.6566 (mm110) REVERT: D 141 ILE cc_start: 0.7717 (mt) cc_final: 0.7485 (mm) REVERT: D 142 SER cc_start: 0.7985 (t) cc_final: 0.7221 (p) REVERT: D 156 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6319 (mm-30) REVERT: D 163 PHE cc_start: 0.7111 (m-80) cc_final: 0.6024 (m-80) REVERT: D 212 MET cc_start: 0.6139 (mmm) cc_final: 0.5829 (mmm) REVERT: D 244 ASP cc_start: 0.6975 (t70) cc_final: 0.6076 (t70) REVERT: D 252 ARG cc_start: 0.7395 (mtp180) cc_final: 0.6559 (ttp-170) REVERT: D 270 THR cc_start: 0.7252 (p) cc_final: 0.7014 (t) REVERT: D 287 THR cc_start: 0.7358 (t) cc_final: 0.7037 (m) REVERT: D 330 LEU cc_start: 0.7625 (mt) cc_final: 0.7063 (mt) REVERT: D 339 ARG cc_start: 0.6784 (mtt180) cc_final: 0.6508 (mmt-90) REVERT: D 345 GLN cc_start: 0.7900 (tt0) cc_final: 0.7395 (tt0) REVERT: D 362 VAL cc_start: 0.7955 (t) cc_final: 0.7657 (p) REVERT: D 374 LEU cc_start: 0.8477 (mt) cc_final: 0.8227 (mt) REVERT: D 387 ASN cc_start: 0.7514 (m-40) cc_final: 0.7306 (m-40) REVERT: D 405 PHE cc_start: 0.7626 (m-10) cc_final: 0.7294 (m-80) REVERT: D 428 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6455 (mt-10) REVERT: D 441 PHE cc_start: 0.8582 (t80) cc_final: 0.7989 (t80) REVERT: D 445 LEU cc_start: 0.8398 (tp) cc_final: 0.8190 (mt) REVERT: D 453 LYS cc_start: 0.7178 (pttt) cc_final: 0.6864 (pttt) REVERT: D 474 ASN cc_start: 0.6537 (p0) cc_final: 0.6173 (p0) REVERT: D 483 ARG cc_start: 0.7330 (ttt90) cc_final: 0.7024 (tpt170) REVERT: D 487 HIS cc_start: 0.7814 (p-80) cc_final: 0.7587 (p-80) REVERT: D 504 ARG cc_start: 0.7432 (mpt180) cc_final: 0.6822 (mpt180) REVERT: D 512 ASP cc_start: 0.7155 (t0) cc_final: 0.6896 (t0) REVERT: D 544 TRP cc_start: 0.8155 (m100) cc_final: 0.7745 (m100) REVERT: D 546 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7617 (ttm-80) REVERT: D 573 HIS cc_start: 0.7320 (m170) cc_final: 0.6784 (m170) REVERT: D 577 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7309 (mmtt) REVERT: E 74 ARG cc_start: 0.7409 (mtt-85) cc_final: 0.7190 (mtt-85) REVERT: E 76 THR cc_start: 0.7615 (m) cc_final: 0.7383 (p) REVERT: E 100 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: E 102 PHE cc_start: 0.7675 (m-80) cc_final: 0.7377 (m-80) REVERT: E 131 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6370 (mt-10) REVERT: E 136 HIS cc_start: 0.7402 (m-70) cc_final: 0.6928 (m-70) REVERT: E 143 ILE cc_start: 0.8284 (mm) cc_final: 0.7968 (tp) REVERT: E 209 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7051 (mm-30) REVERT: E 215 GLN cc_start: 0.7588 (mt0) cc_final: 0.7209 (mt0) REVERT: E 224 SER cc_start: 0.7436 (m) cc_final: 0.7070 (p) REVERT: E 251 GLU cc_start: 0.7258 (tp30) cc_final: 0.6481 (tp30) REVERT: E 256 MET cc_start: 0.7136 (ttp) cc_final: 0.6732 (ttp) REVERT: E 299 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6235 (mt-10) REVERT: E 315 MET cc_start: 0.7046 (mmm) cc_final: 0.6452 (mmm) REVERT: E 326 GLU cc_start: 0.6483 (mt-10) cc_final: 0.6151 (tt0) REVERT: E 330 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7548 (tp) REVERT: E 356 ASP cc_start: 0.6978 (m-30) cc_final: 0.6739 (m-30) REVERT: E 381 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7390 (mm-40) REVERT: E 396 LYS cc_start: 0.7270 (mttt) cc_final: 0.6834 (mtmt) REVERT: E 400 LYS cc_start: 0.8009 (pttt) cc_final: 0.7668 (ptpp) REVERT: E 439 ARG cc_start: 0.7780 (mmt-90) cc_final: 0.7496 (mmt180) REVERT: E 486 PHE cc_start: 0.8019 (t80) cc_final: 0.7608 (t80) REVERT: E 502 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6848 (mt-10) REVERT: E 518 ARG cc_start: 0.8196 (ttp-110) cc_final: 0.7794 (mtp-110) REVERT: E 521 MET cc_start: 0.7130 (mtp) cc_final: 0.6511 (mtp) REVERT: E 525 MET cc_start: 0.7334 (mmt) cc_final: 0.6857 (mmt) REVERT: E 527 PHE cc_start: 0.7039 (p90) cc_final: 0.6709 (p90) REVERT: E 530 SER cc_start: 0.8467 (t) cc_final: 0.7961 (p) REVERT: E 568 SER cc_start: 0.8130 (p) cc_final: 0.7892 (t) REVERT: E 577 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7794 (mtpp) REVERT: E 588 ILE cc_start: 0.8419 (mt) cc_final: 0.7977 (tp) REVERT: H 74 ARG cc_start: 0.7130 (mtt90) cc_final: 0.6710 (mtt-85) REVERT: H 76 THR cc_start: 0.7630 (m) cc_final: 0.7274 (p) REVERT: H 100 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6703 (mm-30) REVERT: H 102 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7769 (m-10) REVERT: H 105 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7887 (ptpp) REVERT: H 111 LYS cc_start: 0.7860 (pttt) cc_final: 0.7399 (pttt) REVERT: H 124 GLN cc_start: 0.7184 (tm-30) cc_final: 0.6568 (tm-30) REVERT: H 130 SER cc_start: 0.8670 (t) cc_final: 0.8118 (p) REVERT: H 140 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.6868 (m-40) REVERT: H 150 LYS cc_start: 0.8049 (tttt) cc_final: 0.7821 (ttmt) REVERT: H 173 ASP cc_start: 0.7411 (m-30) cc_final: 0.7159 (m-30) REVERT: H 215 GLN cc_start: 0.7593 (mt0) cc_final: 0.7185 (mt0) REVERT: H 228 ILE cc_start: 0.8367 (mp) cc_final: 0.8107 (mp) REVERT: H 241 GLN cc_start: 0.8190 (pp30) cc_final: 0.7899 (pp30) REVERT: H 249 ASP cc_start: 0.7020 (m-30) cc_final: 0.6595 (m-30) REVERT: H 256 MET cc_start: 0.7555 (ttp) cc_final: 0.6711 (ttp) REVERT: H 267 ASP cc_start: 0.7321 (t0) cc_final: 0.6783 (t0) REVERT: H 273 LYS cc_start: 0.7545 (tttt) cc_final: 0.7258 (tttt) REVERT: H 303 THR cc_start: 0.8369 (m) cc_final: 0.7614 (t) REVERT: H 314 PHE cc_start: 0.8470 (p90) cc_final: 0.8044 (p90) REVERT: H 315 MET cc_start: 0.7212 (mmm) cc_final: 0.6812 (mmm) REVERT: H 330 LEU cc_start: 0.8218 (tp) cc_final: 0.7831 (tt) REVERT: H 334 ILE cc_start: 0.8352 (mt) cc_final: 0.8150 (mm) REVERT: H 341 GLN cc_start: 0.8094 (tt0) cc_final: 0.7563 (tm-30) REVERT: H 350 MET cc_start: 0.7899 (ptp) cc_final: 0.7643 (ptp) REVERT: H 362 VAL cc_start: 0.8355 (t) cc_final: 0.8016 (p) REVERT: H 364 ARG cc_start: 0.7820 (ptp-170) cc_final: 0.7078 (ptm160) REVERT: H 373 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7517 (ttpp) REVERT: H 381 GLN cc_start: 0.7291 (tp40) cc_final: 0.6712 (mm-40) REVERT: H 394 VAL cc_start: 0.8662 (t) cc_final: 0.8321 (m) REVERT: H 397 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6238 (mm-30) REVERT: H 404 LEU cc_start: 0.8486 (mp) cc_final: 0.8151 (mt) REVERT: H 409 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8648 (mttm) REVERT: H 463 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7145 (mt-10) REVERT: H 502 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6922 (mm-30) REVERT: H 521 MET cc_start: 0.7368 (mtp) cc_final: 0.6888 (mtp) REVERT: H 543 ILE cc_start: 0.7906 (mt) cc_final: 0.7687 (mt) REVERT: H 546 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7608 (ttp80) REVERT: H 593 PHE cc_start: 0.7957 (t80) cc_final: 0.7476 (t80) outliers start: 54 outliers final: 37 residues processed: 644 average time/residue: 0.1389 time to fit residues: 129.9349 Evaluate side-chains 646 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 602 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 486 PHE Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 502 GLU Chi-restraints excluded: chain H residue 517 VAL Chi-restraints excluded: chain H residue 572 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 127 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.0070 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 overall best weight: 1.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 HIS ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 HIS H 136 HIS H 177 ASN H 190 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.138941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120932 restraints weight = 26184.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125387 restraints weight = 13145.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128356 restraints weight = 8018.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130340 restraints weight = 5491.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131600 restraints weight = 4077.425| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17320 Z= 0.198 Angle : 0.645 10.339 23497 Z= 0.338 Chirality : 0.045 0.241 2603 Planarity : 0.004 0.051 2976 Dihedral : 6.131 107.905 2856 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.11 % Allowed : 21.86 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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 (0.19), residues: 1978 helix: 1.33 (0.31), residues: 285 sheet: 0.42 (0.22), residues: 576 loop : -0.48 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 74 TYR 0.033 0.002 TYR E 214 PHE 0.037 0.002 PHE E 55 TRP 0.026 0.002 TRP H 75 HIS 0.005 0.001 HIS D 598 Details of bonding type rmsd covalent geometry : bond 0.00428 (17259) covalent geometry : angle 0.62916 (23366) SS BOND : bond 0.00237 ( 16) SS BOND : angle 1.54518 ( 32) hydrogen bonds : bond 0.04410 ( 560) hydrogen bonds : angle 5.27745 ( 1413) metal coordination : bond 0.01326 ( 12) link_BETA1-4 : bond 0.00391 ( 11) link_BETA1-4 : angle 1.76663 ( 33) link_BETA1-6 : bond 0.00405 ( 4) link_BETA1-6 : angle 1.69961 ( 12) link_NAG-ASN : bond 0.00375 ( 18) link_NAG-ASN : angle 2.46005 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 619 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.7959 (tt) cc_final: 0.7354 (pt) REVERT: A 153 ILE cc_start: 0.8181 (mt) cc_final: 0.7687 (tp) REVERT: A 154 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6867 (mt-10) REVERT: A 156 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6499 (mm-30) REVERT: A 215 GLN cc_start: 0.7204 (tm-30) cc_final: 0.6610 (tm-30) REVERT: A 293 ASP cc_start: 0.6678 (OUTLIER) cc_final: 0.6344 (t0) REVERT: A 315 MET cc_start: 0.6183 (mmm) cc_final: 0.5979 (mmm) REVERT: A 340 LYS cc_start: 0.7516 (mttt) cc_final: 0.7221 (mttt) REVERT: A 372 ARG cc_start: 0.7266 (ttp-110) cc_final: 0.6854 (ptm-80) REVERT: A 375 VAL cc_start: 0.8107 (t) cc_final: 0.7763 (p) REVERT: A 396 LYS cc_start: 0.7815 (mttt) cc_final: 0.7601 (mttt) REVERT: A 428 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6475 (mt-10) REVERT: A 438 VAL cc_start: 0.8304 (t) cc_final: 0.7819 (p) REVERT: A 443 GLN cc_start: 0.7725 (mp10) cc_final: 0.7505 (mp10) REVERT: A 447 ASN cc_start: 0.7803 (m-40) cc_final: 0.7573 (m-40) REVERT: A 469 VAL cc_start: 0.7644 (t) cc_final: 0.6803 (p) REVERT: A 492 GLU cc_start: 0.7002 (pt0) cc_final: 0.6650 (pt0) REVERT: A 493 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7681 (m-40) REVERT: A 527 PHE cc_start: 0.7797 (p90) cc_final: 0.7208 (p90) REVERT: A 530 SER cc_start: 0.8267 (t) cc_final: 0.7810 (p) REVERT: A 583 LYS cc_start: 0.7824 (tptt) cc_final: 0.7540 (tptt) REVERT: A 585 ASP cc_start: 0.6638 (t0) cc_final: 0.6218 (t0) REVERT: D 45 GLU cc_start: 0.7800 (tt0) cc_final: 0.7312 (tt0) REVERT: D 96 LEU cc_start: 0.8231 (mt) cc_final: 0.7903 (mp) REVERT: D 101 MET cc_start: 0.7168 (mmm) cc_final: 0.6374 (mmm) REVERT: D 105 LYS cc_start: 0.8056 (mttt) cc_final: 0.7556 (mtmt) REVERT: D 141 ILE cc_start: 0.7762 (mt) cc_final: 0.7507 (mm) REVERT: D 142 SER cc_start: 0.8024 (t) cc_final: 0.7281 (p) REVERT: D 156 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6458 (mm-30) REVERT: D 163 PHE cc_start: 0.7183 (m-80) cc_final: 0.6143 (m-80) REVERT: D 212 MET cc_start: 0.6236 (mmm) cc_final: 0.5948 (mmm) REVERT: D 215 GLN cc_start: 0.7650 (mt0) cc_final: 0.7313 (mt0) REVERT: D 244 ASP cc_start: 0.7040 (t70) cc_final: 0.6328 (t70) REVERT: D 252 ARG cc_start: 0.7481 (mtp180) cc_final: 0.6648 (ttp-170) REVERT: D 270 THR cc_start: 0.7351 (p) cc_final: 0.7092 (t) REVERT: D 287 THR cc_start: 0.7366 (t) cc_final: 0.7025 (m) REVERT: D 330 LEU cc_start: 0.7492 (mt) cc_final: 0.7013 (mt) REVERT: D 339 ARG cc_start: 0.6939 (mtt180) cc_final: 0.6661 (mmt-90) REVERT: D 345 GLN cc_start: 0.7963 (tt0) cc_final: 0.7460 (tt0) REVERT: D 362 VAL cc_start: 0.8026 (t) cc_final: 0.7741 (p) REVERT: D 374 LEU cc_start: 0.8525 (mt) cc_final: 0.8227 (mt) REVERT: D 387 ASN cc_start: 0.7487 (m-40) cc_final: 0.7265 (m-40) REVERT: D 402 ARG cc_start: 0.6890 (mtt-85) cc_final: 0.6590 (mtt-85) REVERT: D 405 PHE cc_start: 0.7637 (m-10) cc_final: 0.7325 (m-80) REVERT: D 428 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6456 (mt-10) REVERT: D 441 PHE cc_start: 0.8570 (t80) cc_final: 0.7990 (t80) REVERT: D 445 LEU cc_start: 0.8394 (tp) cc_final: 0.8129 (mt) REVERT: D 453 LYS cc_start: 0.7346 (pttt) cc_final: 0.6834 (pttt) REVERT: D 455 GLN cc_start: 0.7766 (mp10) cc_final: 0.7257 (mp10) REVERT: D 470 THR cc_start: 0.8167 (m) cc_final: 0.7625 (p) REVERT: D 474 ASN cc_start: 0.6628 (p0) cc_final: 0.6356 (p0) REVERT: D 483 ARG cc_start: 0.7334 (ttt90) cc_final: 0.7021 (tpt170) REVERT: D 487 HIS cc_start: 0.7862 (p-80) cc_final: 0.7641 (p-80) REVERT: D 492 GLU cc_start: 0.6793 (pt0) cc_final: 0.6560 (pt0) REVERT: D 504 ARG cc_start: 0.7504 (mpt180) cc_final: 0.6887 (mpt180) REVERT: D 512 ASP cc_start: 0.7191 (t0) cc_final: 0.6926 (t0) REVERT: D 544 TRP cc_start: 0.8175 (m100) cc_final: 0.7698 (m100) REVERT: D 546 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7684 (ttm-80) REVERT: D 577 LYS cc_start: 0.7742 (mmtt) cc_final: 0.7339 (mmtt) REVERT: E 74 ARG cc_start: 0.7411 (mtt-85) cc_final: 0.7130 (mtt-85) REVERT: E 76 THR cc_start: 0.7727 (m) cc_final: 0.7470 (p) REVERT: E 100 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6990 (tm-30) REVERT: E 102 PHE cc_start: 0.7720 (m-80) cc_final: 0.7419 (m-80) REVERT: E 131 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6411 (mt-10) REVERT: E 136 HIS cc_start: 0.7425 (m-70) cc_final: 0.6900 (m-70) REVERT: E 143 ILE cc_start: 0.8295 (mm) cc_final: 0.7995 (tp) REVERT: E 154 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6757 (mt-10) REVERT: E 168 SER cc_start: 0.7846 (m) cc_final: 0.7320 (p) REVERT: E 209 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7020 (mm-30) REVERT: E 214 TYR cc_start: 0.7989 (m-80) cc_final: 0.7772 (m-80) REVERT: E 215 GLN cc_start: 0.7598 (mt0) cc_final: 0.7260 (mt0) REVERT: E 224 SER cc_start: 0.7500 (m) cc_final: 0.7132 (p) REVERT: E 234 GLU cc_start: 0.7498 (mp0) cc_final: 0.7255 (mp0) REVERT: E 251 GLU cc_start: 0.7306 (tp30) cc_final: 0.6539 (tp30) REVERT: E 256 MET cc_start: 0.7188 (ttp) cc_final: 0.6622 (ttp) REVERT: E 287 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7733 (m) REVERT: E 299 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6381 (mt-10) REVERT: E 315 MET cc_start: 0.7044 (mmm) cc_final: 0.6400 (mmm) REVERT: E 326 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6295 (tt0) REVERT: E 356 ASP cc_start: 0.6978 (m-30) cc_final: 0.6761 (m-30) REVERT: E 381 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7429 (mm-40) REVERT: E 400 LYS cc_start: 0.8042 (pttt) cc_final: 0.7692 (ptpp) REVERT: E 409 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7889 (ttpp) REVERT: E 486 PHE cc_start: 0.8098 (t80) cc_final: 0.7817 (t80) REVERT: E 502 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6877 (mt-10) REVERT: E 518 ARG cc_start: 0.8251 (ttp-110) cc_final: 0.7857 (mtp85) REVERT: E 521 MET cc_start: 0.7189 (mtp) cc_final: 0.6752 (mtp) REVERT: E 525 MET cc_start: 0.7367 (mmt) cc_final: 0.6887 (mmm) REVERT: E 530 SER cc_start: 0.8492 (t) cc_final: 0.8008 (p) REVERT: E 568 SER cc_start: 0.8192 (p) cc_final: 0.7938 (t) REVERT: E 577 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7810 (mtpp) REVERT: E 588 ILE cc_start: 0.8414 (mt) cc_final: 0.7994 (tp) REVERT: E 594 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6667 (mt-10) REVERT: E 595 ASP cc_start: 0.5994 (t0) cc_final: 0.5476 (t70) REVERT: H 74 ARG cc_start: 0.7154 (mtt90) cc_final: 0.6718 (mtt-85) REVERT: H 76 THR cc_start: 0.7640 (m) cc_final: 0.7280 (p) REVERT: H 102 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7675 (m-10) REVERT: H 105 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7931 (ptpp) REVERT: H 111 LYS cc_start: 0.7887 (pttt) cc_final: 0.7423 (pttt) REVERT: H 124 GLN cc_start: 0.7232 (tm-30) cc_final: 0.6714 (tm-30) REVERT: H 130 SER cc_start: 0.8718 (t) cc_final: 0.8147 (p) REVERT: H 173 ASP cc_start: 0.7426 (m-30) cc_final: 0.7181 (m-30) REVERT: H 215 GLN cc_start: 0.7671 (mt0) cc_final: 0.7276 (mt0) REVERT: H 228 ILE cc_start: 0.8366 (mp) cc_final: 0.8132 (mp) REVERT: H 241 GLN cc_start: 0.8179 (pp30) cc_final: 0.7922 (pp30) REVERT: H 249 ASP cc_start: 0.7063 (m-30) cc_final: 0.6666 (m-30) REVERT: H 256 MET cc_start: 0.7587 (ttp) cc_final: 0.6996 (ttp) REVERT: H 273 LYS cc_start: 0.7600 (tttt) cc_final: 0.7251 (tttt) REVERT: H 303 THR cc_start: 0.8244 (m) cc_final: 0.7488 (t) REVERT: H 314 PHE cc_start: 0.8496 (p90) cc_final: 0.8060 (p90) REVERT: H 315 MET cc_start: 0.7224 (mmm) cc_final: 0.6783 (mmm) REVERT: H 330 LEU cc_start: 0.8190 (tp) cc_final: 0.7829 (tt) REVERT: H 341 GLN cc_start: 0.8126 (tt0) cc_final: 0.7621 (tm-30) REVERT: H 362 VAL cc_start: 0.8384 (t) cc_final: 0.8057 (p) REVERT: H 364 ARG cc_start: 0.7860 (ptp-170) cc_final: 0.7106 (ptm160) REVERT: H 373 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7368 (ttpp) REVERT: H 381 GLN cc_start: 0.7359 (tp40) cc_final: 0.6813 (mm-40) REVERT: H 394 VAL cc_start: 0.8670 (t) cc_final: 0.8322 (m) REVERT: H 397 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6282 (mm-30) REVERT: H 404 LEU cc_start: 0.8497 (mp) cc_final: 0.8172 (mt) REVERT: H 463 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7179 (mt-10) REVERT: H 482 LEU cc_start: 0.8103 (tp) cc_final: 0.7892 (tt) REVERT: H 521 MET cc_start: 0.7407 (mtp) cc_final: 0.6944 (mtp) REVERT: H 543 ILE cc_start: 0.7846 (mt) cc_final: 0.7581 (mt) outliers start: 56 outliers final: 42 residues processed: 647 average time/residue: 0.1416 time to fit residues: 133.5208 Evaluate side-chains 672 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 624 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 599 LEU Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 517 VAL Chi-restraints excluded: chain H residue 572 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 157 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 166 optimal weight: 0.0970 chunk 98 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN A 387 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 HIS D 573 HIS ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 HIS H 136 HIS H 177 ASN H 190 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125157 restraints weight = 26021.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.129653 restraints weight = 13187.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132642 restraints weight = 8078.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.134590 restraints weight = 5555.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135880 restraints weight = 4136.713| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17320 Z= 0.141 Angle : 0.625 13.980 23497 Z= 0.325 Chirality : 0.044 0.238 2603 Planarity : 0.004 0.047 2976 Dihedral : 6.003 106.589 2856 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.72 % Allowed : 22.92 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.09 (0.19), residues: 1978 helix: 1.39 (0.31), residues: 286 sheet: 0.41 (0.22), residues: 568 loop : -0.43 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 549 TYR 0.027 0.001 TYR E 214 PHE 0.031 0.002 PHE E 55 TRP 0.026 0.002 TRP A 361 HIS 0.005 0.001 HIS D 598 Details of bonding type rmsd covalent geometry : bond 0.00312 (17259) covalent geometry : angle 0.61036 (23366) SS BOND : bond 0.00203 ( 16) SS BOND : angle 1.32974 ( 32) hydrogen bonds : bond 0.03884 ( 560) hydrogen bonds : angle 5.20296 ( 1413) metal coordination : bond 0.00829 ( 12) link_BETA1-4 : bond 0.00406 ( 11) link_BETA1-4 : angle 1.73219 ( 33) link_BETA1-6 : bond 0.00479 ( 4) link_BETA1-6 : angle 1.57156 ( 12) link_NAG-ASN : bond 0.00240 ( 18) link_NAG-ASN : angle 2.30397 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 623 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.7906 (tt) cc_final: 0.7308 (pt) REVERT: A 153 ILE cc_start: 0.8156 (mt) cc_final: 0.7662 (tp) REVERT: A 154 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6806 (mt-10) REVERT: A 156 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6524 (mm-30) REVERT: A 215 GLN cc_start: 0.7205 (tm-30) cc_final: 0.6616 (tm-30) REVERT: A 293 ASP cc_start: 0.6763 (m-30) cc_final: 0.6419 (t0) REVERT: A 315 MET cc_start: 0.6204 (mmm) cc_final: 0.5966 (mmm) REVERT: A 316 GLN cc_start: 0.6997 (tt0) cc_final: 0.6714 (tt0) REVERT: A 340 LYS cc_start: 0.7480 (mttt) cc_final: 0.7200 (mttt) REVERT: A 363 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7708 (ttp-170) REVERT: A 372 ARG cc_start: 0.7258 (ttp-110) cc_final: 0.6850 (ptm-80) REVERT: A 375 VAL cc_start: 0.8166 (t) cc_final: 0.7745 (p) REVERT: A 428 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6501 (mt-10) REVERT: A 438 VAL cc_start: 0.8303 (t) cc_final: 0.7819 (p) REVERT: A 447 ASN cc_start: 0.7747 (m-40) cc_final: 0.7539 (m-40) REVERT: A 469 VAL cc_start: 0.7622 (t) cc_final: 0.6793 (p) REVERT: A 493 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7642 (m-40) REVERT: A 527 PHE cc_start: 0.7713 (p90) cc_final: 0.7147 (p90) REVERT: A 530 SER cc_start: 0.8289 (t) cc_final: 0.7826 (p) REVERT: A 583 LYS cc_start: 0.7850 (tptt) cc_final: 0.7575 (tptt) REVERT: A 585 ASP cc_start: 0.6633 (t0) cc_final: 0.6218 (t0) REVERT: D 45 GLU cc_start: 0.7759 (tt0) cc_final: 0.7274 (tt0) REVERT: D 96 LEU cc_start: 0.8199 (mt) cc_final: 0.7858 (mp) REVERT: D 101 MET cc_start: 0.7136 (mmm) cc_final: 0.6344 (mmm) REVERT: D 105 LYS cc_start: 0.7973 (mttt) cc_final: 0.7447 (mtmt) REVERT: D 141 ILE cc_start: 0.7679 (mt) cc_final: 0.7421 (mm) REVERT: D 142 SER cc_start: 0.7998 (t) cc_final: 0.7182 (p) REVERT: D 156 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6406 (mm-30) REVERT: D 163 PHE cc_start: 0.7127 (m-80) cc_final: 0.6483 (m-80) REVERT: D 212 MET cc_start: 0.6165 (mmm) cc_final: 0.5878 (mmm) REVERT: D 215 GLN cc_start: 0.7674 (mt0) cc_final: 0.7330 (mt0) REVERT: D 244 ASP cc_start: 0.7036 (t70) cc_final: 0.6093 (t70) REVERT: D 252 ARG cc_start: 0.7415 (mtp180) cc_final: 0.6946 (tpt90) REVERT: D 270 THR cc_start: 0.7308 (p) cc_final: 0.7039 (t) REVERT: D 287 THR cc_start: 0.7369 (t) cc_final: 0.6952 (m) REVERT: D 301 ASP cc_start: 0.7126 (p0) cc_final: 0.6749 (p0) REVERT: D 330 LEU cc_start: 0.7607 (mt) cc_final: 0.7035 (mt) REVERT: D 345 GLN cc_start: 0.7899 (tt0) cc_final: 0.7426 (tt0) REVERT: D 357 ARG cc_start: 0.7466 (ptm-80) cc_final: 0.7024 (ptm-80) REVERT: D 362 VAL cc_start: 0.8027 (t) cc_final: 0.7737 (p) REVERT: D 374 LEU cc_start: 0.8492 (mt) cc_final: 0.8262 (mt) REVERT: D 389 LYS cc_start: 0.8250 (mttp) cc_final: 0.7993 (mttp) REVERT: D 405 PHE cc_start: 0.7636 (m-10) cc_final: 0.7320 (m-80) REVERT: D 428 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6389 (mt-10) REVERT: D 441 PHE cc_start: 0.8670 (t80) cc_final: 0.8145 (t80) REVERT: D 445 LEU cc_start: 0.8373 (tp) cc_final: 0.8130 (mt) REVERT: D 453 LYS cc_start: 0.7325 (pttt) cc_final: 0.6788 (pttt) REVERT: D 455 GLN cc_start: 0.7740 (mp10) cc_final: 0.7216 (mp10) REVERT: D 470 THR cc_start: 0.8144 (m) cc_final: 0.7625 (p) REVERT: D 474 ASN cc_start: 0.6691 (p0) cc_final: 0.6426 (p0) REVERT: D 487 HIS cc_start: 0.7831 (p-80) cc_final: 0.7614 (p-80) REVERT: D 504 ARG cc_start: 0.7474 (mpt180) cc_final: 0.6839 (mpt180) REVERT: D 512 ASP cc_start: 0.7113 (t0) cc_final: 0.6825 (t0) REVERT: D 544 TRP cc_start: 0.8167 (m100) cc_final: 0.7741 (m100) REVERT: D 577 LYS cc_start: 0.7713 (mmtt) cc_final: 0.7338 (mmtt) REVERT: E 74 ARG cc_start: 0.7385 (mtt-85) cc_final: 0.7117 (mtt-85) REVERT: E 76 THR cc_start: 0.7677 (m) cc_final: 0.7448 (p) REVERT: E 100 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6978 (tm-30) REVERT: E 102 PHE cc_start: 0.7687 (m-80) cc_final: 0.7363 (m-80) REVERT: E 131 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6390 (mt-10) REVERT: E 136 HIS cc_start: 0.7390 (m-70) cc_final: 0.6856 (m-70) REVERT: E 143 ILE cc_start: 0.8242 (mm) cc_final: 0.7911 (tp) REVERT: E 154 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6768 (mt-10) REVERT: E 168 SER cc_start: 0.7771 (m) cc_final: 0.7260 (p) REVERT: E 182 GLN cc_start: 0.7193 (mm-40) cc_final: 0.6872 (mm-40) REVERT: E 209 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7032 (mm-30) REVERT: E 215 GLN cc_start: 0.7633 (mt0) cc_final: 0.7291 (mt0) REVERT: E 224 SER cc_start: 0.7493 (m) cc_final: 0.7106 (p) REVERT: E 234 GLU cc_start: 0.7452 (mp0) cc_final: 0.7224 (mp0) REVERT: E 251 GLU cc_start: 0.7273 (tp30) cc_final: 0.6983 (tp30) REVERT: E 256 MET cc_start: 0.7151 (ttp) cc_final: 0.6648 (ttp) REVERT: E 266 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7950 (mm) REVERT: E 287 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7803 (m) REVERT: E 299 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6246 (mt-10) REVERT: E 301 ASP cc_start: 0.7801 (p0) cc_final: 0.7559 (p0) REVERT: E 315 MET cc_start: 0.7183 (mmm) cc_final: 0.6591 (mmm) REVERT: E 326 GLU cc_start: 0.6609 (mt-10) cc_final: 0.6265 (tt0) REVERT: E 350 MET cc_start: 0.7476 (mtp) cc_final: 0.7229 (mtm) REVERT: E 381 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7442 (mm-40) REVERT: E 409 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7826 (ttpp) REVERT: E 439 ARG cc_start: 0.7706 (mmt-90) cc_final: 0.7470 (mmt180) REVERT: E 486 PHE cc_start: 0.8068 (t80) cc_final: 0.7664 (t80) REVERT: E 502 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6856 (mt-10) REVERT: E 518 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.7854 (mtp85) REVERT: E 521 MET cc_start: 0.7129 (mtp) cc_final: 0.6594 (mtp) REVERT: E 525 MET cc_start: 0.7347 (mmt) cc_final: 0.6876 (mmt) REVERT: E 530 SER cc_start: 0.8495 (t) cc_final: 0.8018 (p) REVERT: E 568 SER cc_start: 0.8182 (p) cc_final: 0.7962 (t) REVERT: E 577 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7810 (mtpp) REVERT: E 588 ILE cc_start: 0.8389 (mt) cc_final: 0.8021 (tp) REVERT: E 594 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6659 (mt-10) REVERT: E 595 ASP cc_start: 0.6009 (t0) cc_final: 0.5506 (t70) REVERT: H 74 ARG cc_start: 0.7156 (mtt90) cc_final: 0.6737 (mtt-85) REVERT: H 76 THR cc_start: 0.7659 (m) cc_final: 0.7308 (p) REVERT: H 102 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7646 (m-10) REVERT: H 105 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7924 (ptpp) REVERT: H 111 LYS cc_start: 0.7880 (pttt) cc_final: 0.7431 (pttt) REVERT: H 130 SER cc_start: 0.8733 (t) cc_final: 0.8169 (p) REVERT: H 140 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.6596 (m-40) REVERT: H 166 GLU cc_start: 0.7150 (tp30) cc_final: 0.6760 (tp30) REVERT: H 173 ASP cc_start: 0.7405 (m-30) cc_final: 0.7165 (m-30) REVERT: H 228 ILE cc_start: 0.8345 (mp) cc_final: 0.8110 (mp) REVERT: H 241 GLN cc_start: 0.8205 (pp30) cc_final: 0.7947 (pp30) REVERT: H 249 ASP cc_start: 0.6991 (m-30) cc_final: 0.6614 (m-30) REVERT: H 256 MET cc_start: 0.7576 (ttp) cc_final: 0.6990 (ttp) REVERT: H 273 LYS cc_start: 0.7561 (tttt) cc_final: 0.7234 (tttt) REVERT: H 303 THR cc_start: 0.8246 (m) cc_final: 0.7513 (t) REVERT: H 314 PHE cc_start: 0.8476 (p90) cc_final: 0.8075 (p90) REVERT: H 315 MET cc_start: 0.7218 (mmm) cc_final: 0.6759 (mmm) REVERT: H 330 LEU cc_start: 0.8190 (tp) cc_final: 0.7820 (tt) REVERT: H 341 GLN cc_start: 0.8101 (tt0) cc_final: 0.7591 (tm-30) REVERT: H 362 VAL cc_start: 0.8366 (t) cc_final: 0.8019 (p) REVERT: H 364 ARG cc_start: 0.7836 (ptp-170) cc_final: 0.7093 (ptm160) REVERT: H 373 LYS cc_start: 0.8056 (ttpp) cc_final: 0.7457 (ttpp) REVERT: H 381 GLN cc_start: 0.7375 (tp40) cc_final: 0.6808 (mm-40) REVERT: H 394 VAL cc_start: 0.8668 (t) cc_final: 0.8313 (m) REVERT: H 397 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6255 (mm-30) REVERT: H 404 LEU cc_start: 0.8499 (mp) cc_final: 0.8181 (mt) REVERT: H 409 LYS cc_start: 0.8904 (mtmt) cc_final: 0.8532 (mttm) REVERT: H 463 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7155 (mt-10) REVERT: H 482 LEU cc_start: 0.8133 (tp) cc_final: 0.7876 (tt) REVERT: H 521 MET cc_start: 0.7416 (mtp) cc_final: 0.6956 (mtp) REVERT: H 543 ILE cc_start: 0.7846 (mt) cc_final: 0.7578 (mt) outliers start: 49 outliers final: 37 residues processed: 647 average time/residue: 0.1429 time to fit residues: 133.1580 Evaluate side-chains 655 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 611 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 599 LEU Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 517 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 9 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 33 optimal weight: 0.0770 chunk 152 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 chunk 113 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 3 optimal weight: 0.0050 chunk 93 optimal weight: 2.9990 overall best weight: 0.7954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 HIS D 573 HIS ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 HIS H 136 HIS H 177 ASN H 190 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124850 restraints weight = 26043.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.129332 restraints weight = 13086.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132311 restraints weight = 7947.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134182 restraints weight = 5441.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.135611 restraints weight = 4055.499| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17320 Z= 0.126 Angle : 0.619 10.056 23497 Z= 0.322 Chirality : 0.044 0.241 2603 Planarity : 0.004 0.046 2976 Dihedral : 5.845 105.075 2856 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.66 % Allowed : 23.53 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.17 (0.19), residues: 1978 helix: 1.52 (0.31), residues: 286 sheet: 0.47 (0.22), residues: 568 loop : -0.41 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 549 TYR 0.021 0.001 TYR H 553 PHE 0.030 0.002 PHE E 55 TRP 0.025 0.002 TRP A 361 HIS 0.005 0.001 HIS E 165 Details of bonding type rmsd covalent geometry : bond 0.00282 (17259) covalent geometry : angle 0.60550 (23366) SS BOND : bond 0.00218 ( 16) SS BOND : angle 1.23495 ( 32) hydrogen bonds : bond 0.03676 ( 560) hydrogen bonds : angle 5.12012 ( 1413) metal coordination : bond 0.00662 ( 12) link_BETA1-4 : bond 0.00394 ( 11) link_BETA1-4 : angle 1.69437 ( 33) link_BETA1-6 : bond 0.00482 ( 4) link_BETA1-6 : angle 1.56079 ( 12) link_NAG-ASN : bond 0.00189 ( 18) link_NAG-ASN : angle 2.21459 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3058.84 seconds wall clock time: 53 minutes 25.52 seconds (3205.52 seconds total)