Starting phenix.real_space_refine on Fri Jul 3 23:34:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uab_26419/07_2026/7uab_26419.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uab_26419/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7uab_26419/07_2026/7uab_26419.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uab_26419/07_2026/7uab_26419.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uab_26419/07_2026/7uab_26419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uab_26419/07_2026/7uab_26419.map" model { file = "/net/cci-nas-00/data/ceres_data/7uab_26419/07_2026/7uab_26419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uab_26419/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 3.13, per 1000 atoms: 0.19 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: 1.58 Conformation dependent library (CDL) restraints added in 610.4 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: 0.58 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: 2.84 Time building geometry restraints manager: 2.03 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 - 17.86: 9121 17.86 - 35.73: 572 35.73 - 53.59: 118 53.59 - 71.46: 25 71.46 - 89.32: 20 Dihedral angle restraints: 9856 sinusoidal: 3960 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 9853 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: 0.670 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.750 Find NCS groups from input model: 0.430 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: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 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 : 13.288 89.320 6002 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/Z covalent geometry : bond 0.01251 / 0.78 (17259) covalent geometry : angle 1.72384 / 1.18 (23366) SS BOND : bond 0.00757 / 0.38 ( 16) SS BOND : angle 2.22841 / 1.33 ( 32) hydrogen bonds : bond 0.18164 / 11.43 ( 560) hydrogen bonds : angle 7.16565 / 4.98 ( 1413) metal coordination : bond 0.32702 / 19.49 ( 12) link_BETA1-4 : bond 0.00922 / 0.51 ( 11) link_BETA1-4 : angle 2.54718 / 1.84 ( 33) link_BETA1-6 : bond 0.00410 / 0.20 ( 4) link_BETA1-6 : angle 2.34084 / 1.30 ( 12) link_NAG-ASN : bond 0.01031 / 0.49 ( 18) link_NAG-ASN : angle 4.00967 / 2.95 ( 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 : 0.624 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: 0.7847 (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: 0.6199 (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: 0.7710 (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: 0.5506 (mmm) REVERT: A 341 GLN cc_start: 0.7743 (tt0) cc_final: 0.7522 (tt0) REVERT: A 345 GLN cc_start: 0.7966 (tt0) cc_final: 0.7451 (tt0) REVERT: A 347 PHE cc_start: 0.8268 (m-80) cc_final: 0.8054 (m-80) REVERT: A 348 TYR cc_start: 0.7721 (p90) cc_final: 0.7330 (p90) REVERT: A 351 THR cc_start: 0.7209 (p) cc_final: 0.6985 (t) REVERT: A 375 VAL cc_start: 0.7962 (t) cc_final: 0.7545 (m) REVERT: A 376 LYS cc_start: 0.7935 (tttt) cc_final: 0.7720 (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: 0.7272 (m90) 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: 0.7014 (m-40) REVERT: A 465 TYR cc_start: 0.7788 (m-80) cc_final: 0.7317 (m-80) REVERT: A 474 ASN cc_start: 0.7510 (m-40) cc_final: 0.7083 (m-40) REVERT: A 521 MET cc_start: 0.6803 (mtp) cc_final: 0.6420 (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: 0.6606 (tpp) REVERT: A 583 LYS cc_start: 0.7851 (tptt) cc_final: 0.7543 (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: 0.4588 (p0) REVERT: D 287 THR cc_start: 0.7048 (t) cc_final: 0.6743 (m) REVERT: D 315 MET cc_start: 0.6417 (mmm) cc_final: 0.6157 (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: 0.7275 (ttp-170) REVERT: D 373 LYS cc_start: 0.8274 (tttt) cc_final: 0.7782 (ttmm) REVERT: D 387 ASN cc_start: 0.7488 (m-40) cc_final: 0.7014 (m-40) REVERT: D 393 VAL cc_start: 0.8012 (t) cc_final: 0.7766 (p) REVERT: D 399 GLN cc_start: 0.6842 (mt0) cc_final: 0.6634 (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: 0.7597 (mt) REVERT: D 442 SER cc_start: 0.7914 (m) cc_final: 0.7096 (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: 0.6625 (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: 0.7684 (mm) REVERT: E 156 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6330 (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: 0.6182 (mmm) REVERT: E 224 SER cc_start: 0.6923 (m) cc_final: 0.6502 (p) REVERT: E 234 GLU cc_start: 0.7302 (mp0) cc_final: 0.7074 (mp0) REVERT: E 241 GLN cc_start: 0.7715 (pp30) cc_final: 0.7321 (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: 0.5648 (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: 0.7391 (p0) REVERT: E 303 THR cc_start: 0.8238 (m) cc_final: 0.8002 (t) REVERT: E 304 LEU cc_start: 0.7996 (mt) cc_final: 0.7722 (mt) REVERT: E 315 MET cc_start: 0.7452 (mmm) cc_final: 0.7132 (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: 0.7752 (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: 0.6599 (mt-10) REVERT: E 474 ASN cc_start: 0.7501 (m-40) cc_final: 0.6916 (p0) REVERT: E 486 PHE cc_start: 0.7695 (t80) cc_final: 0.7192 (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: 0.7536 (tt0) REVERT: E 521 MET cc_start: 0.7041 (mtp) cc_final: 0.5463 (mtp) REVERT: E 525 MET cc_start: 0.7331 (mmt) cc_final: 0.7036 (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: 0.7732 (tt) REVERT: E 590 PHE cc_start: 0.8271 (m-10) cc_final: 0.8038 (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: 0.6395 (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: 0.7545 (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: 0.6826 (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: 0.6273 (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: 0.7191 (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: 0.6892 (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: 0.7049 (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: 0.7183 (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: 0.6873 (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: 0.6735 (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: 0.7686 (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: 0.8060 (mm) REVERT: H 521 MET cc_start: 0.7157 (mtp) cc_final: 0.6564 (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: 0.6165 (tpp) REVERT: H 581 PHE cc_start: 0.8168 (m-80) cc_final: 0.7853 (m-80) REVERT: H 583 LYS cc_start: 0.7647 (tttp) cc_final: 0.7393 (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: 0.1298 time to fit residues: 144.8695 Evaluate side-chains 625 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 621 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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... A 72 ASN A 123 GLN A 139 GLN A 189 HIS A 316 GLN A 342 GLN A 505 GLN A 554 HIS D 86 ASN D 341 GLN D 345 GLN D 386 HIS 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 Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.151277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132078 restraints weight = 26107.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136550 restraints weight = 13337.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.139570 restraints weight = 8233.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141675 restraints weight = 5726.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.143252 restraints weight = 4309.110| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17320 Z= 0.150 Angle : 0.673 14.615 23497 Z= 0.348 Chirality : 0.047 0.212 2603 Planarity : 0.004 0.055 2976 Dihedral : 5.536 32.947 2185 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.33 % Allowed : 11.65 % 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: 0.32 (0.18), residues: 1978 helix: 1.06 (0.30), residues: 288 sheet: 0.67 (0.21), residues: 575 loop : -0.21 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.018 0.002 TYR E 465 PHE 0.025 0.002 PHE A 527 TRP 0.020 0.002 TRP A 361 HIS 0.012 0.002 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (17259) covalent geometry : angle 0.64943 / 0.34 (23366) SS BOND : bond 0.00219 / 0.14 ( 16) SS BOND : angle 1.55140 / 0.95 ( 32) hydrogen bonds : bond 0.04658 / 3.00 ( 560) hydrogen bonds : angle 5.63560 / 3.91 ( 1413) metal coordination : bond 0.02528 / 1.50 ( 12) link_BETA1-4 : bond 0.00485 / 0.31 ( 11) link_BETA1-4 : angle 1.82863 / 1.16 ( 33) link_BETA1-6 : bond 0.00419 / 0.21 ( 4) link_BETA1-6 : angle 1.84072 / 1.07 ( 12) link_NAG-ASN : bond 0.00381 / 0.21 ( 18) link_NAG-ASN : angle 3.25334 / 2.40 ( 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 681 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 639 time to evaluate : 0.507 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: A 95 ILE cc_start: 0.7671 (mt) cc_final: 0.7347 (mm) REVERT: A 113 TYR cc_start: 0.7315 (t80) cc_final: 0.7059 (t80) REVERT: A 121 ILE cc_start: 0.7717 (tt) cc_final: 0.7114 (pt) REVERT: A 141 ILE cc_start: 0.8150 (mt) cc_final: 0.7864 (mm) REVERT: A 156 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6295 (mm-30) REVERT: A 188 GLN cc_start: 0.7851 (pm20) cc_final: 0.7465 (pm20) REVERT: A 190 ASN cc_start: 0.8049 (m-40) cc_final: 0.7834 (m110) REVERT: A 271 PHE cc_start: 0.8086 (m-10) cc_final: 0.7626 (m-10) REVERT: A 293 ASP cc_start: 0.6281 (p0) cc_final: 0.5735 (p0) REVERT: A 314 PHE cc_start: 0.7986 (p90) cc_final: 0.7366 (p90) REVERT: A 315 MET cc_start: 0.6375 (mmm) cc_final: 0.5639 (mmm) REVERT: A 317 PHE cc_start: 0.7829 (t80) cc_final: 0.7285 (t80) REVERT: A 345 GLN cc_start: 0.7999 (tt0) cc_final: 0.7701 (tt0) REVERT: A 359 VAL cc_start: 0.8220 (t) cc_final: 0.7885 (m) REVERT: A 363 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7447 (ttp-110) REVERT: A 372 ARG cc_start: 0.7149 (ttp-110) cc_final: 0.6776 (ptm-80) REVERT: A 375 VAL cc_start: 0.8103 (t) cc_final: 0.7722 (p) REVERT: A 385 ASP cc_start: 0.6404 (t0) cc_final: 0.6153 (t0) REVERT: A 396 LYS cc_start: 0.7965 (mttt) cc_final: 0.7557 (mttt) REVERT: A 447 ASN cc_start: 0.7501 (m-40) cc_final: 0.7198 (m-40) REVERT: A 460 TYR cc_start: 0.8460 (m-10) cc_final: 0.8035 (m-10) REVERT: A 465 TYR cc_start: 0.7728 (m-80) cc_final: 0.7457 (m-80) REVERT: A 474 ASN cc_start: 0.7820 (m-40) cc_final: 0.7528 (m-40) REVERT: A 498 GLU cc_start: 0.6713 (tt0) cc_final: 0.6510 (tt0) REVERT: A 502 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6575 (mt-10) REVERT: A 505 GLN cc_start: 0.7850 (tt0) cc_final: 0.7563 (tt0) REVERT: A 527 PHE cc_start: 0.8041 (p90) cc_final: 0.7557 (p90) REVERT: A 529 THR cc_start: 0.7957 (p) cc_final: 0.7705 (p) REVERT: A 575 MET cc_start: 0.6582 (tpp) cc_final: 0.6210 (tpp) REVERT: A 583 LYS cc_start: 0.7821 (tptt) cc_final: 0.7446 (tptt) REVERT: A 585 ASP cc_start: 0.6438 (t0) cc_final: 0.6121 (t0) REVERT: D 135 GLN cc_start: 0.7266 (mm-40) cc_final: 0.6978 (mm-40) REVERT: D 141 ILE cc_start: 0.7839 (mt) cc_final: 0.7450 (mm) REVERT: D 163 PHE cc_start: 0.7014 (m-80) cc_final: 0.6412 (m-80) REVERT: D 212 MET cc_start: 0.6238 (mmm) cc_final: 0.5757 (mmm) REVERT: D 242 ARG cc_start: 0.7119 (mmt180) cc_final: 0.6718 (mmt-90) REVERT: D 244 ASP cc_start: 0.6962 (t70) cc_final: 0.6512 (t70) REVERT: D 252 ARG cc_start: 0.7536 (mtp180) cc_final: 0.6773 (mtp180) REVERT: D 270 THR cc_start: 0.7342 (p) cc_final: 0.7102 (t) REVERT: D 285 ASP cc_start: 0.5142 (p0) cc_final: 0.4757 (p0) REVERT: D 287 THR cc_start: 0.7325 (t) cc_final: 0.6840 (m) REVERT: D 315 MET cc_start: 0.6453 (mmm) cc_final: 0.6220 (mmm) REVERT: D 316 GLN cc_start: 0.6584 (tm-30) cc_final: 0.6369 (tm-30) REVERT: D 330 LEU cc_start: 0.7573 (mt) cc_final: 0.7034 (mt) REVERT: D 355 SER cc_start: 0.7725 (m) cc_final: 0.7415 (p) REVERT: D 393 VAL cc_start: 0.7877 (t) cc_final: 0.7540 (p) REVERT: D 396 LYS cc_start: 0.7715 (mttt) cc_final: 0.7390 (mttt) REVERT: D 428 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6460 (mt-10) REVERT: D 441 PHE cc_start: 0.8505 (t80) cc_final: 0.7650 (t80) REVERT: D 445 LEU cc_start: 0.8262 (tp) cc_final: 0.7998 (mt) REVERT: D 453 LYS cc_start: 0.6797 (pttt) cc_final: 0.6134 (pttt) REVERT: D 460 TYR cc_start: 0.8384 (m-80) cc_final: 0.8043 (m-10) REVERT: D 486 PHE cc_start: 0.7904 (t80) cc_final: 0.7344 (t80) REVERT: D 502 GLU cc_start: 0.7188 (mt-10) cc_final: 0.5920 (mt-10) REVERT: D 512 ASP cc_start: 0.7175 (t0) cc_final: 0.6899 (t0) REVERT: D 531 LYS cc_start: 0.7690 (mttp) cc_final: 0.7115 (mttp) REVERT: D 573 HIS cc_start: 0.7187 (m170) cc_final: 0.6199 (m170) REVERT: D 577 LYS cc_start: 0.7446 (mmtt) cc_final: 0.7177 (mmtt) REVERT: E 73 THR cc_start: 0.7722 (p) cc_final: 0.6948 (m) REVERT: E 101 MET cc_start: 0.7690 (mmm) cc_final: 0.7314 (mmm) REVERT: E 131 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6482 (mt-10) REVERT: E 136 HIS cc_start: 0.6926 (m-70) cc_final: 0.6447 (m-70) REVERT: E 153 ILE cc_start: 0.7816 (mt) cc_final: 0.7589 (mm) REVERT: E 156 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6435 (mm-30) REVERT: E 182 GLN cc_start: 0.7387 (mm110) cc_final: 0.7180 (mm-40) REVERT: E 215 GLN cc_start: 0.7322 (mt0) cc_final: 0.7032 (mt0) REVERT: E 234 GLU cc_start: 0.7336 (mp0) cc_final: 0.7084 (mp0) REVERT: E 241 GLN cc_start: 0.7861 (pp30) cc_final: 0.7516 (pp30) REVERT: E 256 MET cc_start: 0.6815 (ttp) cc_final: 0.6518 (ttp) REVERT: E 265 LEU cc_start: 0.8242 (tp) cc_final: 0.7966 (tp) REVERT: E 266 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8058 (mm) REVERT: E 279 MET cc_start: 0.7562 (mtp) cc_final: 0.7353 (mtp) REVERT: E 299 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6296 (mm-30) REVERT: E 303 THR cc_start: 0.8453 (m) cc_final: 0.7835 (t) REVERT: E 304 LEU cc_start: 0.7991 (mt) cc_final: 0.7650 (mt) REVERT: E 315 MET cc_start: 0.7322 (mmm) cc_final: 0.6917 (mmm) REVERT: E 336 TYR cc_start: 0.8041 (m-80) cc_final: 0.7834 (m-80) REVERT: E 400 LYS cc_start: 0.7989 (pttt) cc_final: 0.7656 (ptpp) REVERT: E 409 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7600 (ttpp) REVERT: E 412 PRO cc_start: 0.8780 (Cg_endo) cc_final: 0.8367 (Cg_exo) REVERT: E 428 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7089 (mt-10) REVERT: E 474 ASN cc_start: 0.7703 (m-40) cc_final: 0.7272 (m-40) REVERT: E 486 PHE cc_start: 0.7775 (t80) cc_final: 0.7359 (t80) REVERT: E 518 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7697 (mtp-110) REVERT: E 521 MET cc_start: 0.7100 (mtp) cc_final: 0.6412 (mtp) REVERT: E 525 MET cc_start: 0.7253 (mmt) cc_final: 0.6851 (mmt) REVERT: E 577 LYS cc_start: 0.7701 (mtpp) cc_final: 0.7471 (mtpp) REVERT: E 588 ILE cc_start: 0.8405 (mt) cc_final: 0.7900 (tt) REVERT: H 74 ARG cc_start: 0.7034 (mtt90) cc_final: 0.6449 (mtt-85) REVERT: H 76 THR cc_start: 0.7689 (m) cc_final: 0.7367 (p) REVERT: H 81 TYR cc_start: 0.7920 (p90) cc_final: 0.7399 (p90) REVERT: H 100 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6960 (mm-30) REVERT: H 101 MET cc_start: 0.7510 (mmm) cc_final: 0.7231 (mmm) REVERT: H 111 LYS cc_start: 0.7873 (pttt) cc_final: 0.7244 (pttt) REVERT: H 124 GLN cc_start: 0.6959 (tt0) cc_final: 0.6687 (tm-30) REVERT: H 130 SER cc_start: 0.8306 (t) cc_final: 0.7888 (p) REVERT: H 134 ASP cc_start: 0.6800 (t0) cc_final: 0.6537 (t0) REVERT: H 154 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6561 (mt-10) REVERT: H 173 ASP cc_start: 0.7528 (m-30) cc_final: 0.7256 (m-30) REVERT: H 190 ASN cc_start: 0.8217 (m-40) cc_final: 0.7887 (m-40) REVERT: H 207 ASP cc_start: 0.6410 (t0) cc_final: 0.6133 (t0) REVERT: H 209 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6930 (mt-10) REVERT: H 212 MET cc_start: 0.7087 (mmm) cc_final: 0.6778 (mmm) REVERT: H 218 SER cc_start: 0.8187 (m) cc_final: 0.7883 (p) REVERT: H 241 GLN cc_start: 0.7709 (pp30) cc_final: 0.7144 (pp30) REVERT: H 245 PHE cc_start: 0.7861 (m-80) cc_final: 0.6834 (m-10) REVERT: H 252 ARG cc_start: 0.7584 (ttm170) cc_final: 0.7337 (mtm-85) REVERT: H 256 MET cc_start: 0.7361 (ttp) cc_final: 0.6848 (ttp) REVERT: H 275 ASN cc_start: 0.7527 (p0) cc_final: 0.7291 (p0) REVERT: H 315 MET cc_start: 0.7290 (mmm) cc_final: 0.6980 (mmm) REVERT: H 331 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6502 (mt-10) REVERT: H 338 LYS cc_start: 0.7901 (mttt) cc_final: 0.7618 (mttt) REVERT: H 349 LYS cc_start: 0.8249 (ttpt) cc_final: 0.8006 (ttpt) REVERT: H 364 ARG cc_start: 0.7652 (ptp-170) cc_final: 0.7264 (ptm160) REVERT: H 381 GLN cc_start: 0.7016 (tp40) cc_final: 0.6625 (mm-40) REVERT: H 394 VAL cc_start: 0.8494 (t) cc_final: 0.8261 (m) REVERT: H 397 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6290 (mm-30) REVERT: H 404 LEU cc_start: 0.8450 (mp) cc_final: 0.7786 (mt) REVERT: H 471 LEU cc_start: 0.7946 (tp) cc_final: 0.7562 (tp) REVERT: H 498 GLU cc_start: 0.7039 (tt0) cc_final: 0.6694 (tt0) REVERT: H 519 ASN cc_start: 0.6837 (m-40) cc_final: 0.6636 (m110) REVERT: H 521 MET cc_start: 0.7419 (mtp) cc_final: 0.6894 (mtp) REVERT: H 575 MET cc_start: 0.6625 (tpp) cc_final: 0.6419 (tpp) REVERT: H 592 ASP cc_start: 0.6753 (m-30) cc_final: 0.6329 (m-30) REVERT: H 593 PHE cc_start: 0.8003 (t80) cc_final: 0.7409 (t80) outliers start: 42 outliers final: 25 residues processed: 662 average time/residue: 0.1259 time to fit residues: 121.9585 Evaluate side-chains 637 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 611 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 398 GLU Chi-restraints excluded: chain D residue 422 ASP 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 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 445 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: 2.9990 chunk 121 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 145 optimal weight: 0.0770 chunk 29 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN A 139 GLN A 381 GLN A 406 GLN A 487 HIS D 86 ASN D 443 GLN D 493 ASN ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 HIS H 47 ASN H 220 ASN H 302 HIS H 341 GLN H 474 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.140922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122062 restraints weight = 26716.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126741 restraints weight = 13374.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129817 restraints weight = 8110.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131845 restraints weight = 5547.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133372 restraints weight = 4126.100| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17320 Z= 0.121 Angle : 0.575 8.079 23497 Z= 0.304 Chirality : 0.044 0.205 2603 Planarity : 0.004 0.038 2976 Dihedral : 4.852 21.595 2179 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.16 % Allowed : 14.21 % Favored : 82.63 % 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: 0.55 (0.18), residues: 1978 helix: 1.42 (0.31), residues: 295 sheet: 0.77 (0.21), residues: 565 loop : -0.07 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 458 TYR 0.023 0.001 TYR H 553 PHE 0.023 0.002 PHE E 99 TRP 0.020 0.002 TRP A 361 HIS 0.008 0.001 HIS H 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (17259) covalent geometry : angle 0.55649 / 0.30 (23366) SS BOND : bond 0.00262 / 0.15 ( 16) SS BOND : angle 1.14866 / 0.69 ( 32) hydrogen bonds : bond 0.04077 / 2.64 ( 560) hydrogen bonds : angle 5.24519 / 3.61 ( 1413) metal coordination : bond 0.00858 / 0.56 ( 12) link_BETA1-4 : bond 0.00487 / 0.31 ( 11) link_BETA1-4 : angle 1.63256 / 0.97 ( 33) link_BETA1-6 : bond 0.00575 / 0.28 ( 4) link_BETA1-6 : angle 1.30618 / 0.77 ( 12) link_NAG-ASN : bond 0.00220 / 0.13 ( 18) link_NAG-ASN : angle 2.65497 / 2.00 ( 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 683 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 626 time to evaluate : 0.564 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 113 TYR cc_start: 0.7491 (t80) cc_final: 0.7228 (t80) REVERT: A 121 ILE cc_start: 0.7711 (tt) cc_final: 0.7159 (pt) REVERT: A 141 ILE cc_start: 0.8080 (mt) cc_final: 0.7808 (mm) REVERT: A 156 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6356 (mm-30) REVERT: A 271 PHE cc_start: 0.8055 (m-10) cc_final: 0.7707 (m-10) REVERT: A 315 MET cc_start: 0.6429 (mmm) cc_final: 0.5646 (mmm) REVERT: A 317 PHE cc_start: 0.7849 (t80) cc_final: 0.7225 (t80) REVERT: A 363 ARG cc_start: 0.7881 (ttm170) cc_final: 0.7582 (ttp-110) REVERT: A 372 ARG cc_start: 0.7137 (ttp-110) cc_final: 0.6710 (ptm-80) REVERT: A 375 VAL cc_start: 0.8162 (t) cc_final: 0.7812 (p) REVERT: A 415 SER cc_start: 0.6915 (t) cc_final: 0.6688 (t) REVERT: A 443 GLN cc_start: 0.7786 (mp10) cc_final: 0.7250 (mp10) REVERT: A 447 ASN cc_start: 0.7545 (m-40) cc_final: 0.7267 (m-40) REVERT: A 460 TYR cc_start: 0.8450 (m-10) cc_final: 0.8086 (m-80) REVERT: A 465 TYR cc_start: 0.7813 (m-80) cc_final: 0.7303 (m-80) REVERT: A 474 ASN cc_start: 0.8021 (m-40) cc_final: 0.7815 (m110) REVERT: A 498 GLU cc_start: 0.6702 (tt0) cc_final: 0.6494 (tt0) REVERT: A 502 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6668 (mt-10) REVERT: A 529 THR cc_start: 0.7988 (p) cc_final: 0.7746 (p) REVERT: A 583 LYS cc_start: 0.7844 (tptt) cc_final: 0.7494 (tptt) REVERT: A 585 ASP cc_start: 0.6401 (t0) cc_final: 0.6124 (t0) REVERT: D 45 GLU cc_start: 0.7754 (tt0) cc_final: 0.7297 (tt0) REVERT: D 74 ARG cc_start: 0.7240 (mtt-85) cc_final: 0.6972 (mmt-90) REVERT: D 79 ILE cc_start: 0.7385 (mm) cc_final: 0.6368 (tt) REVERT: D 85 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6771 (t0) REVERT: D 105 LYS cc_start: 0.8222 (mttt) cc_final: 0.7800 (mttt) REVERT: D 141 ILE cc_start: 0.7884 (mt) cc_final: 0.7560 (mm) REVERT: D 142 SER cc_start: 0.8019 (t) cc_final: 0.7465 (p) REVERT: D 155 HIS cc_start: 0.7321 (t70) cc_final: 0.6963 (t70) REVERT: D 215 GLN cc_start: 0.7613 (mt0) cc_final: 0.7377 (mt0) REVERT: D 244 ASP cc_start: 0.6975 (t70) cc_final: 0.6479 (t70) REVERT: D 270 THR cc_start: 0.7287 (p) cc_final: 0.7049 (t) REVERT: D 285 ASP cc_start: 0.5350 (p0) cc_final: 0.5109 (p0) REVERT: D 287 THR cc_start: 0.7366 (t) cc_final: 0.6834 (m) REVERT: D 315 MET cc_start: 0.6424 (mmm) cc_final: 0.6008 (mmm) REVERT: D 330 LEU cc_start: 0.7609 (mt) cc_final: 0.7091 (mt) REVERT: D 355 SER cc_start: 0.7659 (m) cc_final: 0.7354 (p) REVERT: D 396 LYS cc_start: 0.7749 (mttt) cc_final: 0.7429 (mttt) REVERT: D 400 LYS cc_start: 0.7813 (pttt) cc_final: 0.7553 (pttt) REVERT: D 405 PHE cc_start: 0.7633 (m-10) cc_final: 0.7327 (m-10) REVERT: D 428 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6420 (mm-30) REVERT: D 441 PHE cc_start: 0.8472 (t80) cc_final: 0.7797 (t80) REVERT: D 445 LEU cc_start: 0.8270 (tp) cc_final: 0.8014 (mt) REVERT: D 453 LYS cc_start: 0.6763 (pttt) cc_final: 0.6439 (pttt) REVERT: D 460 TYR cc_start: 0.8346 (m-80) cc_final: 0.8087 (m-10) REVERT: D 465 TYR cc_start: 0.7612 (m-80) cc_final: 0.7078 (m-80) REVERT: D 486 PHE cc_start: 0.7842 (t80) cc_final: 0.7447 (t80) REVERT: D 487 HIS cc_start: 0.7432 (p-80) cc_final: 0.7187 (p-80) REVERT: D 512 ASP cc_start: 0.7117 (t0) cc_final: 0.6874 (t0) REVERT: D 546 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7546 (ttm-80) REVERT: D 573 HIS cc_start: 0.7208 (m170) cc_final: 0.6248 (m170) REVERT: D 577 LYS cc_start: 0.7546 (mmtt) cc_final: 0.7264 (mmtt) REVERT: E 74 ARG cc_start: 0.7409 (mtt-85) cc_final: 0.7132 (mtt-85) REVERT: E 100 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6878 (tm-30) REVERT: E 131 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6424 (mt-10) REVERT: E 136 HIS cc_start: 0.7192 (m-70) cc_final: 0.6780 (m-70) REVERT: E 143 ILE cc_start: 0.8529 (mm) cc_final: 0.8258 (tp) REVERT: E 173 ASP cc_start: 0.7736 (m-30) cc_final: 0.7529 (t0) REVERT: E 215 GLN cc_start: 0.7452 (mt0) cc_final: 0.7131 (mt0) REVERT: E 221 LYS cc_start: 0.8243 (ttpt) cc_final: 0.8015 (ptpp) REVERT: E 234 GLU cc_start: 0.7292 (mp0) cc_final: 0.7056 (mp0) REVERT: E 241 GLN cc_start: 0.7867 (pp30) cc_final: 0.7622 (pp30) REVERT: E 244 ASP cc_start: 0.7350 (t0) cc_final: 0.7144 (t0) REVERT: E 251 GLU cc_start: 0.7321 (tp30) cc_final: 0.6676 (tp30) REVERT: E 256 MET cc_start: 0.7142 (ttp) cc_final: 0.6646 (ttp) REVERT: E 279 MET cc_start: 0.7581 (mtp) cc_final: 0.7369 (mtp) REVERT: E 299 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6230 (mt-10) REVERT: E 303 THR cc_start: 0.8425 (m) cc_final: 0.7839 (t) REVERT: E 304 LEU cc_start: 0.7949 (mt) cc_final: 0.7742 (mt) REVERT: E 315 MET cc_start: 0.7308 (mmm) cc_final: 0.6917 (mmm) REVERT: E 320 SER cc_start: 0.8263 (p) cc_final: 0.7778 (t) REVERT: E 326 GLU cc_start: 0.6012 (mt-10) cc_final: 0.5793 (mt-10) REVERT: E 400 LYS cc_start: 0.7991 (pttt) cc_final: 0.7688 (ptpp) REVERT: E 409 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7771 (ttpp) REVERT: E 412 PRO cc_start: 0.8704 (Cg_endo) cc_final: 0.8411 (Cg_exo) REVERT: E 474 ASN cc_start: 0.7766 (m-40) cc_final: 0.7531 (m-40) REVERT: E 486 PHE cc_start: 0.7912 (t80) cc_final: 0.7491 (t80) REVERT: E 518 ARG cc_start: 0.8023 (ttp-110) cc_final: 0.7635 (mtp-110) REVERT: E 521 MET cc_start: 0.7204 (mtp) cc_final: 0.6571 (mtp) REVERT: E 525 MET cc_start: 0.7291 (mmt) cc_final: 0.6833 (mmt) REVERT: E 546 ARG cc_start: 0.7900 (ttm-80) cc_final: 0.7574 (ttm-80) REVERT: E 577 LYS cc_start: 0.7908 (mtpp) cc_final: 0.7594 (mtpp) REVERT: E 588 ILE cc_start: 0.8400 (mt) cc_final: 0.7928 (tp) REVERT: H 74 ARG cc_start: 0.7099 (mtt90) cc_final: 0.6596 (mtt-85) REVERT: H 76 THR cc_start: 0.7710 (m) cc_final: 0.7351 (p) REVERT: H 100 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7027 (mm-30) REVERT: H 111 LYS cc_start: 0.7871 (pttt) cc_final: 0.7381 (pttt) REVERT: H 130 SER cc_start: 0.8381 (t) cc_final: 0.7840 (p) REVERT: H 154 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6574 (mt-10) REVERT: H 173 ASP cc_start: 0.7472 (m-30) cc_final: 0.7250 (m-30) REVERT: H 180 TRP cc_start: 0.7358 (m100) cc_final: 0.7134 (m100) REVERT: H 207 ASP cc_start: 0.6500 (t0) cc_final: 0.6183 (t0) REVERT: H 209 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6895 (mt-10) REVERT: H 212 MET cc_start: 0.6999 (mmm) cc_final: 0.6600 (mmm) REVERT: H 218 SER cc_start: 0.8214 (m) cc_final: 0.7999 (p) REVERT: H 241 GLN cc_start: 0.7941 (pp30) cc_final: 0.7500 (pp30) REVERT: H 245 PHE cc_start: 0.7869 (m-80) cc_final: 0.6424 (m-80) REVERT: H 249 ASP cc_start: 0.6999 (m-30) cc_final: 0.6462 (m-30) REVERT: H 252 ARG cc_start: 0.7559 (ttm170) cc_final: 0.7290 (mtm-85) REVERT: H 254 ASN cc_start: 0.7822 (m-40) cc_final: 0.7606 (m-40) REVERT: H 256 MET cc_start: 0.7426 (ttp) cc_final: 0.6860 (ttp) REVERT: H 267 ASP cc_start: 0.7302 (t0) cc_final: 0.6783 (t0) REVERT: H 275 ASN cc_start: 0.7485 (p0) cc_final: 0.7226 (p0) REVERT: H 303 THR cc_start: 0.8220 (m) cc_final: 0.7663 (t) REVERT: H 315 MET cc_start: 0.7349 (mmm) cc_final: 0.6917 (mmm) REVERT: H 334 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8170 (tp) REVERT: H 338 LYS cc_start: 0.7989 (mttt) cc_final: 0.7667 (mttt) REVERT: H 364 ARG cc_start: 0.7725 (ptp-170) cc_final: 0.7145 (ptm160) REVERT: H 381 GLN cc_start: 0.7234 (tp40) cc_final: 0.6743 (mm-40) REVERT: H 394 VAL cc_start: 0.8570 (t) cc_final: 0.8237 (m) REVERT: H 397 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6162 (mm-30) REVERT: H 404 LEU cc_start: 0.8414 (mp) cc_final: 0.8016 (mt) REVERT: H 471 LEU cc_start: 0.7960 (tp) cc_final: 0.7596 (tp) REVERT: H 498 GLU cc_start: 0.7098 (tt0) cc_final: 0.6728 (tt0) REVERT: H 521 MET cc_start: 0.7451 (mtp) cc_final: 0.6922 (mtp) REVERT: H 575 MET cc_start: 0.6691 (tpp) cc_final: 0.6405 (tpp) REVERT: H 592 ASP cc_start: 0.6737 (m-30) cc_final: 0.6328 (m-30) REVERT: H 593 PHE cc_start: 0.8012 (t80) cc_final: 0.7603 (t80) REVERT: H 597 THR cc_start: 0.7709 (m) cc_final: 0.7425 (p) outliers start: 57 outliers final: 26 residues processed: 650 average time/residue: 0.1233 time to fit residues: 117.0723 Evaluate side-chains 621 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 592 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 400 LYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 168 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 46 ILE Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 334 ILE Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 435 VAL Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 482 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: 0.0270 chunk 143 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS A 139 GLN A 302 HIS A 406 GLN A 487 HIS A 598 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 139 GLN D 302 HIS D 399 GLN D 493 ASN E 139 GLN E 182 GLN E 268 HIS H 136 HIS H 302 HIS H 519 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.138462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.119841 restraints weight = 26660.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.124492 restraints weight = 13319.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127568 restraints weight = 8055.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129670 restraints weight = 5479.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.131129 restraints weight = 4031.725| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17320 Z= 0.164 Angle : 0.585 7.751 23497 Z= 0.310 Chirality : 0.044 0.208 2603 Planarity : 0.004 0.039 2976 Dihedral : 4.863 32.234 2177 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.83 % Allowed : 16.09 % Favored : 81.08 % 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: 0.39 (0.18), residues: 1978 helix: 1.38 (0.31), residues: 295 sheet: 0.62 (0.21), residues: 568 loop : -0.18 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 578 TYR 0.021 0.002 TYR H 553 PHE 0.018 0.002 PHE E 593 TRP 0.028 0.002 TRP H 567 HIS 0.008 0.001 HIS H 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (17259) covalent geometry : angle 0.56660 / 0.31 (23366) SS BOND : bond 0.00285 / 0.13 ( 16) SS BOND : angle 1.45333 / 0.82 ( 32) hydrogen bonds : bond 0.04168 / 2.72 ( 560) hydrogen bonds : angle 5.23305 / 3.59 ( 1413) metal coordination : bond 0.01224 / 0.80 ( 12) link_BETA1-4 : bond 0.00537 / 0.36 ( 11) link_BETA1-4 : angle 1.64336 / 0.99 ( 33) link_BETA1-6 : bond 0.00284 / 0.14 ( 4) link_BETA1-6 : angle 1.28692 / 0.75 ( 12) link_NAG-ASN : bond 0.00298 / 0.18 ( 18) link_NAG-ASN : angle 2.58450 / 1.95 ( 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 677 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 626 time to evaluate : 0.434 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: A 90 ASN cc_start: 0.7694 (p0) cc_final: 0.7446 (p0) REVERT: A 113 TYR cc_start: 0.7568 (t80) cc_final: 0.7360 (t80) REVERT: A 121 ILE cc_start: 0.7769 (tt) cc_final: 0.7240 (pt) REVERT: A 141 ILE cc_start: 0.8092 (mt) cc_final: 0.7829 (mm) REVERT: A 154 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6744 (mt-10) REVERT: A 156 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6518 (mm-30) REVERT: A 293 ASP cc_start: 0.6472 (p0) cc_final: 0.5979 (p0) REVERT: A 315 MET cc_start: 0.6425 (mmm) cc_final: 0.5728 (mmm) REVERT: A 363 ARG cc_start: 0.8039 (ttm170) cc_final: 0.7629 (ttp-110) REVERT: A 375 VAL cc_start: 0.8076 (t) cc_final: 0.7705 (p) REVERT: A 392 HIS cc_start: 0.8054 (m90) cc_final: 0.7645 (m90) REVERT: A 428 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6449 (mt-10) REVERT: A 447 ASN cc_start: 0.7605 (m-40) cc_final: 0.7331 (m-40) REVERT: A 458 ARG cc_start: 0.8064 (mtm110) cc_final: 0.7712 (ttp80) REVERT: A 465 TYR cc_start: 0.7862 (m-80) cc_final: 0.7437 (m-80) REVERT: A 471 LEU cc_start: 0.8392 (tp) cc_final: 0.8172 (tp) REVERT: A 502 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6615 (mt-10) REVERT: A 527 PHE cc_start: 0.7936 (p90) cc_final: 0.7454 (p90) REVERT: A 583 LYS cc_start: 0.7864 (tptt) cc_final: 0.7535 (tptt) REVERT: A 585 ASP cc_start: 0.6499 (t0) cc_final: 0.6198 (t0) REVERT: D 45 GLU cc_start: 0.7778 (tt0) cc_final: 0.7305 (tt0) REVERT: D 79 ILE cc_start: 0.7430 (mm) cc_final: 0.6542 (tt) REVERT: D 85 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.7081 (t0) REVERT: D 92 LYS cc_start: 0.8138 (mttt) cc_final: 0.7898 (mttt) REVERT: D 101 MET cc_start: 0.7071 (mmm) cc_final: 0.6798 (mmm) REVERT: D 105 LYS cc_start: 0.8174 (mttt) cc_final: 0.7846 (mtmt) REVERT: D 109 ASP cc_start: 0.6857 (t0) cc_final: 0.6652 (t0) REVERT: D 123 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6480 (mm-40) REVERT: D 125 PHE cc_start: 0.7336 (m-10) cc_final: 0.6432 (m-10) REVERT: D 141 ILE cc_start: 0.7892 (mt) cc_final: 0.7603 (mm) REVERT: D 142 SER cc_start: 0.8162 (t) cc_final: 0.7177 (p) REVERT: D 156 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6309 (mm-30) REVERT: D 244 ASP cc_start: 0.7142 (t70) cc_final: 0.6527 (t70) REVERT: D 270 THR cc_start: 0.7313 (p) cc_final: 0.7053 (t) REVERT: D 285 ASP cc_start: 0.5675 (p0) cc_final: 0.5363 (p0) REVERT: D 287 THR cc_start: 0.7408 (t) cc_final: 0.6845 (m) REVERT: D 315 MET cc_start: 0.6444 (mmm) cc_final: 0.6062 (mmm) REVERT: D 330 LEU cc_start: 0.7548 (mt) cc_final: 0.7118 (mt) REVERT: D 356 ASP cc_start: 0.6654 (m-30) cc_final: 0.6121 (m-30) REVERT: D 393 VAL cc_start: 0.8020 (t) cc_final: 0.7682 (p) REVERT: D 396 LYS cc_start: 0.7748 (mttt) cc_final: 0.7427 (mttt) REVERT: D 405 PHE cc_start: 0.7624 (m-10) cc_final: 0.7279 (m-10) REVERT: D 428 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6535 (mt-10) REVERT: D 441 PHE cc_start: 0.8508 (t80) cc_final: 0.7795 (t80) REVERT: D 445 LEU cc_start: 0.8250 (tp) cc_final: 0.8019 (mt) REVERT: D 453 LYS cc_start: 0.6843 (pttt) cc_final: 0.6434 (pttt) REVERT: D 465 TYR cc_start: 0.7727 (m-80) cc_final: 0.7146 (m-80) REVERT: D 486 PHE cc_start: 0.7881 (t80) cc_final: 0.7449 (t80) REVERT: D 487 HIS cc_start: 0.7613 (p-80) cc_final: 0.7320 (p-80) REVERT: D 502 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6810 (mt-10) REVERT: D 512 ASP cc_start: 0.7098 (t0) cc_final: 0.6827 (t0) REVERT: D 546 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7616 (ttm-80) REVERT: D 573 HIS cc_start: 0.7286 (m170) cc_final: 0.6821 (m170) REVERT: D 577 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7325 (mmtt) REVERT: E 74 ARG cc_start: 0.7433 (mtt-85) cc_final: 0.7105 (mtt-85) REVERT: E 76 THR cc_start: 0.7707 (m) cc_final: 0.7495 (p) REVERT: E 100 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7023 (tm-30) REVERT: E 111 LYS cc_start: 0.7791 (pttt) cc_final: 0.7555 (ptmt) REVERT: E 131 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6658 (mt-10) REVERT: E 135 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7505 (mm110) REVERT: E 136 HIS cc_start: 0.7387 (m-70) cc_final: 0.6889 (m-70) REVERT: E 143 ILE cc_start: 0.8496 (mm) cc_final: 0.8178 (tp) REVERT: E 173 ASP cc_start: 0.7803 (m-30) cc_final: 0.7597 (t0) REVERT: E 221 LYS cc_start: 0.8272 (ttpt) cc_final: 0.8033 (ptpp) REVERT: E 234 GLU cc_start: 0.7341 (mp0) cc_final: 0.7094 (mp0) REVERT: E 241 GLN cc_start: 0.8052 (pp30) cc_final: 0.7807 (pp30) REVERT: E 251 GLU cc_start: 0.7324 (tp30) cc_final: 0.6544 (tp30) REVERT: E 256 MET cc_start: 0.7182 (ttp) cc_final: 0.6373 (ttp) REVERT: E 279 MET cc_start: 0.7551 (mtp) cc_final: 0.7347 (mtp) REVERT: E 299 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6245 (mt-10) REVERT: E 303 THR cc_start: 0.8430 (m) cc_final: 0.7769 (t) REVERT: E 304 LEU cc_start: 0.7949 (mt) cc_final: 0.7722 (mt) REVERT: E 315 MET cc_start: 0.7247 (mmm) cc_final: 0.6919 (mmm) REVERT: E 320 SER cc_start: 0.8300 (p) cc_final: 0.7869 (t) REVERT: E 326 GLU cc_start: 0.6258 (mt-10) cc_final: 0.5995 (mt-10) REVERT: E 356 ASP cc_start: 0.6966 (m-30) cc_final: 0.6639 (m-30) REVERT: E 409 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7537 (ttpp) REVERT: E 412 PRO cc_start: 0.8707 (Cg_endo) cc_final: 0.8239 (Cg_exo) REVERT: E 442 SER cc_start: 0.7776 (m) cc_final: 0.7569 (p) REVERT: E 486 PHE cc_start: 0.7966 (t80) cc_final: 0.7555 (t80) REVERT: E 518 ARG cc_start: 0.8199 (ttp-110) cc_final: 0.7805 (mtp-110) REVERT: E 521 MET cc_start: 0.7200 (mtp) cc_final: 0.6655 (mtp) REVERT: E 525 MET cc_start: 0.7280 (mmt) cc_final: 0.6881 (mmt) REVERT: E 530 SER cc_start: 0.8252 (t) cc_final: 0.7674 (p) REVERT: E 546 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7602 (ttm-80) REVERT: E 577 LYS cc_start: 0.7965 (mtpp) cc_final: 0.7630 (mtpp) REVERT: E 588 ILE cc_start: 0.8442 (mt) cc_final: 0.7971 (tp) REVERT: H 74 ARG cc_start: 0.7107 (mtt90) cc_final: 0.6634 (mtt-85) REVERT: H 76 THR cc_start: 0.7748 (m) cc_final: 0.7394 (p) REVERT: H 100 GLU cc_start: 0.7299 (mm-30) cc_final: 0.7026 (mm-30) REVERT: H 111 LYS cc_start: 0.7862 (pttt) cc_final: 0.7385 (pttt) REVERT: H 130 SER cc_start: 0.8472 (t) cc_final: 0.7909 (p) REVERT: H 154 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6447 (mt-10) REVERT: H 166 GLU cc_start: 0.7354 (tp30) cc_final: 0.6770 (tp30) REVERT: H 167 GLN cc_start: 0.8152 (pp30) cc_final: 0.7722 (pm20) REVERT: H 173 ASP cc_start: 0.7500 (m-30) cc_final: 0.7194 (m-30) REVERT: H 207 ASP cc_start: 0.6548 (t0) cc_final: 0.6270 (t0) REVERT: H 209 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6928 (mt-10) REVERT: H 212 MET cc_start: 0.7035 (mmm) cc_final: 0.6748 (mmm) REVERT: H 215 GLN cc_start: 0.7403 (mt0) cc_final: 0.7071 (mt0) REVERT: H 218 SER cc_start: 0.8219 (m) cc_final: 0.7990 (p) REVERT: H 241 GLN cc_start: 0.8090 (pp30) cc_final: 0.7595 (pp30) REVERT: H 242 ARG cc_start: 0.7584 (mmt180) cc_final: 0.7299 (mmt180) REVERT: H 245 PHE cc_start: 0.7792 (m-80) cc_final: 0.6361 (m-80) REVERT: H 249 ASP cc_start: 0.7013 (m-30) cc_final: 0.6477 (m-30) REVERT: H 252 ARG cc_start: 0.7532 (ttm170) cc_final: 0.7237 (mtm-85) REVERT: H 254 ASN cc_start: 0.7924 (m-40) cc_final: 0.7657 (m-40) REVERT: H 256 MET cc_start: 0.7479 (ttp) cc_final: 0.6971 (ttp) REVERT: H 267 ASP cc_start: 0.7329 (t0) cc_final: 0.6797 (t0) REVERT: H 275 ASN cc_start: 0.7467 (p0) cc_final: 0.7135 (p0) REVERT: H 303 THR cc_start: 0.8213 (m) cc_final: 0.7583 (t) REVERT: H 314 PHE cc_start: 0.8511 (p90) cc_final: 0.8129 (p90) REVERT: H 315 MET cc_start: 0.7323 (mmm) cc_final: 0.6932 (mmm) REVERT: H 341 GLN cc_start: 0.7987 (tt0) cc_final: 0.7477 (tm-30) REVERT: H 364 ARG cc_start: 0.7786 (ptp-170) cc_final: 0.7400 (ptm160) REVERT: H 381 GLN cc_start: 0.7283 (tp40) cc_final: 0.6636 (mm-40) REVERT: H 394 VAL cc_start: 0.8447 (t) cc_final: 0.8086 (m) REVERT: H 397 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6359 (mm-30) REVERT: H 404 LEU cc_start: 0.8415 (mp) cc_final: 0.8005 (mt) REVERT: H 463 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6941 (mt-10) REVERT: H 467 PHE cc_start: 0.8154 (p90) cc_final: 0.7797 (p90) REVERT: H 471 LEU cc_start: 0.8048 (tp) cc_final: 0.7734 (tp) REVERT: H 521 MET cc_start: 0.7464 (mtp) cc_final: 0.6854 (mtp) REVERT: H 575 MET cc_start: 0.6737 (tpp) cc_final: 0.6444 (tpp) REVERT: H 592 ASP cc_start: 0.6750 (m-30) cc_final: 0.6491 (m-30) REVERT: H 593 PHE cc_start: 0.8016 (t80) cc_final: 0.7683 (t80) REVERT: H 594 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6533 (mm-30) outliers start: 51 outliers final: 34 residues processed: 648 average time/residue: 0.1305 time to fit residues: 122.3655 Evaluate side-chains 637 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 600 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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 461 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 123 GLN 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 469 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 261 THR 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 379 THR 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 542 VAL Chi-restraints excluded: chain H residue 46 ILE 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 368 THR Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 496 ILE 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: 0.9990 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 199 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN A 487 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN D 190 ASN D 302 HIS D 519 ASN E 165 HIS H 136 HIS H 177 ASN H 302 HIS H 341 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.140073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121608 restraints weight = 26498.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126183 restraints weight = 13440.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129182 restraints weight = 8222.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.131173 restraints weight = 5670.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.132490 restraints weight = 4218.991| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.280 17320 Z= 0.230 Angle : 0.617 8.066 23497 Z= 0.327 Chirality : 0.046 0.203 2603 Planarity : 0.004 0.043 2976 Dihedral : 5.060 30.460 2177 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.22 % Allowed : 16.59 % Favored : 80.19 % 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: 0.19 (0.18), residues: 1978 helix: 1.32 (0.31), residues: 293 sheet: 0.48 (0.21), residues: 576 loop : -0.35 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 364 TYR 0.027 0.002 TYR E 214 PHE 0.019 0.002 PHE D 314 TRP 0.052 0.002 TRP H 567 HIS 0.008 0.001 HIS H 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.22 (17259) covalent geometry : angle 0.59893 / 0.32 (23366) SS BOND : bond 0.00254 / 0.14 ( 16) SS BOND : angle 1.50802 / 0.91 ( 32) hydrogen bonds : bond 0.04618 / 3.02 ( 560) hydrogen bonds : angle 5.26142 / 3.61 ( 1413) metal coordination : bond 0.08223 / 3.97 ( 12) link_BETA1-4 : bond 0.00611 / 0.41 ( 11) link_BETA1-4 : angle 1.65508 / 1.00 ( 33) link_BETA1-6 : bond 0.00257 / 0.13 ( 4) link_BETA1-6 : angle 1.28670 / 0.76 ( 12) link_NAG-ASN : bond 0.00399 / 0.22 ( 18) link_NAG-ASN : angle 2.65719 / 2.00 ( 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 691 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 633 time to evaluate : 0.644 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 82 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8256 (tp) REVERT: A 130 SER cc_start: 0.7526 (t) cc_final: 0.6629 (t) REVERT: A 141 ILE cc_start: 0.8182 (mt) cc_final: 0.7977 (mm) REVERT: A 153 ILE cc_start: 0.8243 (mt) cc_final: 0.7723 (tp) REVERT: A 154 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6842 (mt-10) REVERT: A 156 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6485 (mm-30) REVERT: A 271 PHE cc_start: 0.8107 (m-10) cc_final: 0.7495 (m-10) REVERT: A 293 ASP cc_start: 0.6568 (p0) cc_final: 0.6337 (t0) REVERT: A 315 MET cc_start: 0.6303 (mmm) cc_final: 0.5710 (mmm) REVERT: A 330 LEU cc_start: 0.7966 (tp) cc_final: 0.7573 (tp) REVERT: A 345 GLN cc_start: 0.7960 (tt0) cc_final: 0.7735 (tt0) REVERT: A 375 VAL cc_start: 0.8072 (t) cc_final: 0.7728 (p) REVERT: A 376 LYS cc_start: 0.8101 (tttt) cc_final: 0.7698 (tttt) REVERT: A 428 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6483 (mt-10) REVERT: A 447 ASN cc_start: 0.7741 (m-40) cc_final: 0.7408 (m-40) REVERT: A 458 ARG cc_start: 0.8147 (mtm110) cc_final: 0.7831 (ttp80) REVERT: A 502 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6630 (mt-10) REVERT: A 527 PHE cc_start: 0.7840 (p90) cc_final: 0.7445 (p90) REVERT: A 583 LYS cc_start: 0.7881 (tptt) cc_final: 0.7542 (tptt) REVERT: A 585 ASP cc_start: 0.6634 (t0) cc_final: 0.6316 (t0) REVERT: D 45 GLU cc_start: 0.7875 (tt0) cc_final: 0.7381 (tt0) REVERT: D 79 ILE cc_start: 0.7489 (mm) cc_final: 0.7170 (mt) REVERT: D 85 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7168 (t0) REVERT: D 92 LYS cc_start: 0.8188 (mttt) cc_final: 0.7983 (mttt) REVERT: D 95 ILE cc_start: 0.7881 (mt) cc_final: 0.7662 (mm) REVERT: D 101 MET cc_start: 0.7105 (mmm) cc_final: 0.6644 (mmm) REVERT: D 105 LYS cc_start: 0.8108 (mttt) cc_final: 0.7743 (mtmt) REVERT: D 123 GLN cc_start: 0.7131 (mm-40) cc_final: 0.6680 (mm-40) REVERT: D 135 GLN cc_start: 0.7151 (mm110) cc_final: 0.6753 (mm110) REVERT: D 141 ILE cc_start: 0.7952 (mt) cc_final: 0.7679 (mm) REVERT: D 142 SER cc_start: 0.8130 (t) cc_final: 0.7316 (p) REVERT: D 156 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6390 (mm-30) REVERT: D 190 ASN cc_start: 0.7933 (m110) cc_final: 0.7729 (m-40) REVERT: D 244 ASP cc_start: 0.7105 (t70) cc_final: 0.6519 (t70) REVERT: D 270 THR cc_start: 0.7385 (p) cc_final: 0.7114 (t) REVERT: D 287 THR cc_start: 0.7408 (t) cc_final: 0.6871 (m) REVERT: D 315 MET cc_start: 0.6367 (mmm) cc_final: 0.5900 (mmm) REVERT: D 330 LEU cc_start: 0.7480 (mt) cc_final: 0.6994 (mt) REVERT: D 362 VAL cc_start: 0.7912 (t) cc_final: 0.7539 (p) REVERT: D 396 LYS cc_start: 0.7778 (mttt) cc_final: 0.7507 (mttt) REVERT: D 405 PHE cc_start: 0.7673 (m-10) cc_final: 0.7261 (m-80) REVERT: D 428 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6487 (mt-10) REVERT: D 441 PHE cc_start: 0.8559 (t80) cc_final: 0.8038 (t80) REVERT: D 445 LEU cc_start: 0.8301 (tp) cc_final: 0.8022 (mt) REVERT: D 453 LYS cc_start: 0.7070 (pttt) cc_final: 0.6726 (pttt) REVERT: D 487 HIS cc_start: 0.7772 (p-80) cc_final: 0.7534 (p-80) REVERT: D 502 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6848 (mt-10) REVERT: D 512 ASP cc_start: 0.7184 (t0) cc_final: 0.6937 (t0) REVERT: D 546 ARG cc_start: 0.7888 (ttm-80) cc_final: 0.7660 (ttm-80) REVERT: D 573 HIS cc_start: 0.7302 (m170) cc_final: 0.6982 (m170) REVERT: D 577 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7360 (mmtt) REVERT: E 100 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: E 111 LYS cc_start: 0.7947 (pttt) cc_final: 0.7733 (ptmt) REVERT: E 131 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6531 (mt-10) REVERT: E 136 HIS cc_start: 0.7467 (m-70) cc_final: 0.7056 (m-70) REVERT: E 143 ILE cc_start: 0.8463 (mm) cc_final: 0.8183 (tp) REVERT: E 215 GLN cc_start: 0.7549 (mt0) cc_final: 0.7212 (mt0) REVERT: E 224 SER cc_start: 0.7111 (m) cc_final: 0.6636 (p) REVERT: E 234 GLU cc_start: 0.7516 (mp0) cc_final: 0.7241 (mp0) REVERT: E 241 GLN cc_start: 0.8130 (pp30) cc_final: 0.7817 (pp30) REVERT: E 251 GLU cc_start: 0.7350 (tp30) cc_final: 0.6541 (tp30) REVERT: E 256 MET cc_start: 0.7191 (ttp) cc_final: 0.6800 (ttp) REVERT: E 279 MET cc_start: 0.7526 (mtp) cc_final: 0.7293 (mtp) REVERT: E 299 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6215 (mt-10) REVERT: E 303 THR cc_start: 0.8364 (m) cc_final: 0.7619 (t) REVERT: E 320 SER cc_start: 0.8345 (p) cc_final: 0.8003 (t) REVERT: E 321 SER cc_start: 0.7341 (p) cc_final: 0.7067 (t) REVERT: E 326 GLU cc_start: 0.6459 (mt-10) cc_final: 0.6144 (tt0) REVERT: E 336 TYR cc_start: 0.8301 (m-80) cc_final: 0.8025 (m-80) REVERT: E 356 ASP cc_start: 0.7011 (m-30) cc_final: 0.6791 (m-30) REVERT: E 381 GLN cc_start: 0.7546 (tp40) cc_final: 0.7132 (mm-40) REVERT: E 396 LYS cc_start: 0.7522 (mttt) cc_final: 0.7256 (mtmt) REVERT: E 409 LYS cc_start: 0.8375 (mtpt) cc_final: 0.7532 (ttpt) REVERT: E 412 PRO cc_start: 0.8748 (Cg_endo) cc_final: 0.8390 (Cg_exo) REVERT: E 463 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6561 (mt-10) REVERT: E 486 PHE cc_start: 0.8057 (t80) cc_final: 0.7676 (t80) REVERT: E 502 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6748 (mt-10) REVERT: E 518 ARG cc_start: 0.8279 (ttp-110) cc_final: 0.7845 (mtp-110) REVERT: E 521 MET cc_start: 0.7234 (mtp) cc_final: 0.6741 (mtp) REVERT: E 525 MET cc_start: 0.7366 (mmt) cc_final: 0.6946 (mmt) REVERT: E 530 SER cc_start: 0.8366 (t) cc_final: 0.7788 (p) REVERT: E 568 SER cc_start: 0.8125 (p) cc_final: 0.7875 (t) REVERT: E 577 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7664 (mtpp) REVERT: E 588 ILE cc_start: 0.8460 (mt) cc_final: 0.8004 (tt) REVERT: H 74 ARG cc_start: 0.7157 (mtt90) cc_final: 0.6542 (mtt-85) REVERT: H 76 THR cc_start: 0.7680 (m) cc_final: 0.7350 (p) REVERT: H 100 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7147 (mm-30) REVERT: H 111 LYS cc_start: 0.7856 (pttt) cc_final: 0.7367 (pttt) REVERT: H 124 GLN cc_start: 0.7123 (tm-30) cc_final: 0.6528 (tm-30) REVERT: H 154 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6473 (mt-10) REVERT: H 166 GLU cc_start: 0.7327 (tp30) cc_final: 0.6812 (tp30) REVERT: H 173 ASP cc_start: 0.7457 (m-30) cc_final: 0.7216 (m-30) REVERT: H 209 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7172 (mt-10) REVERT: H 212 MET cc_start: 0.7069 (mmm) cc_final: 0.6829 (mmm) REVERT: H 215 GLN cc_start: 0.7450 (mt0) cc_final: 0.7088 (mt0) REVERT: H 241 GLN cc_start: 0.8128 (pp30) cc_final: 0.7741 (pp30) REVERT: H 242 ARG cc_start: 0.7763 (mmt180) cc_final: 0.7508 (mmt180) REVERT: H 245 PHE cc_start: 0.7776 (m-80) cc_final: 0.6278 (m-80) REVERT: H 249 ASP cc_start: 0.6984 (m-30) cc_final: 0.6525 (m-30) REVERT: H 254 ASN cc_start: 0.8054 (m-40) cc_final: 0.7811 (m-40) REVERT: H 256 MET cc_start: 0.7519 (ttp) cc_final: 0.6787 (ttp) REVERT: H 273 LYS cc_start: 0.7601 (tttt) cc_final: 0.7263 (tptt) REVERT: H 275 ASN cc_start: 0.7466 (p0) cc_final: 0.7155 (p0) REVERT: H 289 TRP cc_start: 0.8485 (m100) cc_final: 0.8238 (m100) REVERT: H 303 THR cc_start: 0.8218 (m) cc_final: 0.7527 (t) REVERT: H 314 PHE cc_start: 0.8487 (p90) cc_final: 0.8042 (p90) REVERT: H 315 MET cc_start: 0.7257 (mmm) cc_final: 0.6809 (mmm) REVERT: H 341 GLN cc_start: 0.8057 (tt0) cc_final: 0.7616 (tm-30) REVERT: H 350 MET cc_start: 0.7935 (ptp) cc_final: 0.7726 (ptp) REVERT: H 364 ARG cc_start: 0.7878 (ptp-170) cc_final: 0.7417 (ptm160) REVERT: H 381 GLN cc_start: 0.7300 (tp40) cc_final: 0.6784 (mm-40) REVERT: H 394 VAL cc_start: 0.8430 (t) cc_final: 0.8093 (m) REVERT: H 397 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6340 (mm-30) REVERT: H 404 LEU cc_start: 0.8516 (mp) cc_final: 0.8164 (mt) REVERT: H 463 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6992 (mt-10) REVERT: H 467 PHE cc_start: 0.8172 (p90) cc_final: 0.7966 (p90) REVERT: H 471 LEU cc_start: 0.8117 (tp) cc_final: 0.7813 (tp) REVERT: H 521 MET cc_start: 0.7477 (mtp) cc_final: 0.6895 (mtp) REVERT: H 575 MET cc_start: 0.6761 (tpp) cc_final: 0.6547 (tpp) REVERT: H 593 PHE cc_start: 0.8017 (t80) cc_final: 0.7697 (t80) REVERT: H 594 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6504 (mm-30) outliers start: 58 outliers final: 39 residues processed: 660 average time/residue: 0.1247 time to fit residues: 120.2005 Evaluate side-chains 646 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 604 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 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 220 ASN Chi-restraints excluded: chain A residue 263 HIS 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 572 SER Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 139 GLN 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 E residue 100 GLU 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 379 THR 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 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 132 VAL 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 372 ARG Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 496 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 39 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 104 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS D 302 HIS D 399 GLN D 493 ASN ** E 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 HIS H 177 ASN H 190 ASN H 302 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123523 restraints weight = 26101.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.128024 restraints weight = 13057.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130949 restraints weight = 7911.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133005 restraints weight = 5407.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134295 restraints weight = 3985.709| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17320 Z= 0.132 Angle : 0.573 7.526 23497 Z= 0.302 Chirality : 0.044 0.198 2603 Planarity : 0.004 0.046 2976 Dihedral : 4.803 28.803 2177 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.16 % Allowed : 17.70 % Favored : 79.13 % 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: 0.26 (0.18), residues: 1978 helix: 1.48 (0.31), residues: 293 sheet: 0.58 (0.22), residues: 564 loop : -0.35 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 549 TYR 0.031 0.001 TYR E 214 PHE 0.030 0.002 PHE D 486 TRP 0.068 0.002 TRP H 567 HIS 0.008 0.001 HIS H 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (17259) covalent geometry : angle 0.55645 / 0.30 (23366) SS BOND : bond 0.00193 / 0.12 ( 16) SS BOND : angle 1.36855 / 0.82 ( 32) hydrogen bonds : bond 0.03847 / 2.52 ( 560) hydrogen bonds : angle 5.13580 / 3.53 ( 1413) metal coordination : bond 0.00766 / 0.49 ( 12) link_BETA1-4 : bond 0.00490 / 0.33 ( 11) link_BETA1-4 : angle 1.55098 / 0.93 ( 33) link_BETA1-6 : bond 0.00364 / 0.19 ( 4) link_BETA1-6 : angle 1.23561 / 0.74 ( 12) link_NAG-ASN : bond 0.00216 / 0.12 ( 18) link_NAG-ASN : angle 2.39518 / 1.81 ( 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 683 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 626 time to evaluate : 0.619 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: 0.7654 (p0) cc_final: 0.7439 (p0) REVERT: A 130 SER cc_start: 0.7369 (t) cc_final: 0.6381 (t) REVERT: A 141 ILE cc_start: 0.8133 (mt) cc_final: 0.7932 (mm) REVERT: A 153 ILE cc_start: 0.8188 (mt) cc_final: 0.7682 (tp) REVERT: A 154 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6845 (mt-10) REVERT: A 156 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6543 (mm-30) REVERT: A 293 ASP cc_start: 0.6582 (p0) cc_final: 0.6345 (t0) REVERT: A 302 HIS cc_start: 0.8463 (t-170) cc_final: 0.8222 (t-170) REVERT: A 330 LEU cc_start: 0.7969 (tp) cc_final: 0.7579 (tp) REVERT: A 362 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7754 (m) REVERT: A 376 LYS cc_start: 0.8046 (tttt) cc_final: 0.7589 (tttt) REVERT: A 428 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6491 (mt-10) REVERT: A 447 ASN cc_start: 0.7727 (m-40) cc_final: 0.7396 (m-40) REVERT: A 458 ARG cc_start: 0.8115 (mtm110) cc_final: 0.7828 (ttp80) REVERT: A 527 PHE cc_start: 0.7844 (p90) cc_final: 0.7299 (p90) REVERT: A 583 LYS cc_start: 0.7842 (tptt) cc_final: 0.7512 (tptt) REVERT: A 585 ASP cc_start: 0.6601 (t0) cc_final: 0.6290 (t0) REVERT: D 45 GLU cc_start: 0.7843 (tt0) cc_final: 0.7335 (tt0) REVERT: D 79 ILE cc_start: 0.7489 (mm) cc_final: 0.7200 (mt) REVERT: D 101 MET cc_start: 0.7079 (mmm) cc_final: 0.6726 (mmm) REVERT: D 105 LYS cc_start: 0.8035 (mttt) cc_final: 0.7675 (mtmt) REVERT: D 123 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6403 (mm110) REVERT: D 125 PHE cc_start: 0.7213 (m-10) cc_final: 0.6548 (m-10) REVERT: D 135 GLN cc_start: 0.7171 (mm110) cc_final: 0.6773 (mm110) REVERT: D 141 ILE cc_start: 0.7916 (mt) cc_final: 0.7489 (mm) REVERT: D 142 SER cc_start: 0.8053 (t) cc_final: 0.7200 (p) REVERT: D 156 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6278 (mm-30) REVERT: D 190 ASN cc_start: 0.7915 (m110) cc_final: 0.7647 (m-40) REVERT: D 242 ARG cc_start: 0.7435 (mmt180) cc_final: 0.7232 (mmt-90) REVERT: D 244 ASP cc_start: 0.7095 (t70) cc_final: 0.6425 (t70) REVERT: D 270 THR cc_start: 0.7329 (p) cc_final: 0.7042 (t) REVERT: D 287 THR cc_start: 0.7381 (t) cc_final: 0.7037 (m) REVERT: D 315 MET cc_start: 0.6376 (mmm) cc_final: 0.5924 (mmm) REVERT: D 330 LEU cc_start: 0.7621 (mt) cc_final: 0.7048 (mt) REVERT: D 362 VAL cc_start: 0.7912 (t) cc_final: 0.7691 (p) REVERT: D 404 LEU cc_start: 0.7749 (mp) cc_final: 0.7455 (mt) REVERT: D 405 PHE cc_start: 0.7641 (m-10) cc_final: 0.7309 (m-80) REVERT: D 428 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6527 (mt-10) REVERT: D 441 PHE cc_start: 0.8544 (t80) cc_final: 0.8015 (t80) REVERT: D 445 LEU cc_start: 0.8271 (tp) cc_final: 0.8026 (mt) REVERT: D 453 LYS cc_start: 0.7092 (pttt) cc_final: 0.6766 (pttt) REVERT: D 512 ASP cc_start: 0.7154 (t0) cc_final: 0.6873 (t0) REVERT: D 544 TRP cc_start: 0.8003 (m100) cc_final: 0.7683 (m100) REVERT: D 573 HIS cc_start: 0.7212 (m170) cc_final: 0.6675 (m170) REVERT: D 577 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7324 (mmtt) REVERT: D 588 ILE cc_start: 0.8632 (mt) cc_final: 0.8380 (mm) REVERT: D 599 LEU cc_start: 0.7906 (mt) cc_final: 0.7659 (mt) REVERT: E 74 ARG cc_start: 0.7507 (mtt-85) cc_final: 0.7303 (mtt-85) REVERT: E 76 THR cc_start: 0.7645 (m) cc_final: 0.7409 (p) REVERT: E 100 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: E 131 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6554 (mt-10) REVERT: E 135 GLN cc_start: 0.7604 (mm-40) cc_final: 0.7278 (mm110) REVERT: E 136 HIS cc_start: 0.7420 (m-70) cc_final: 0.7012 (m-70) REVERT: E 143 ILE cc_start: 0.8414 (mm) cc_final: 0.8101 (tp) REVERT: E 167 GLN cc_start: 0.7208 (pm20) cc_final: 0.6904 (pm20) REVERT: E 220 ASN cc_start: 0.8173 (p0) cc_final: 0.7812 (p0) REVERT: E 224 SER cc_start: 0.7168 (m) cc_final: 0.6687 (p) REVERT: E 234 GLU cc_start: 0.7494 (mp0) cc_final: 0.7234 (mp0) REVERT: E 241 GLN cc_start: 0.8192 (pp30) cc_final: 0.7836 (pp30) REVERT: E 251 GLU cc_start: 0.7326 (tp30) cc_final: 0.6508 (tp30) REVERT: E 256 MET cc_start: 0.7110 (ttp) cc_final: 0.6608 (ttp) REVERT: E 279 MET cc_start: 0.7521 (mtp) cc_final: 0.7301 (mtp) REVERT: E 299 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6155 (mt-10) REVERT: E 303 THR cc_start: 0.8397 (m) cc_final: 0.7843 (t) REVERT: E 320 SER cc_start: 0.8386 (p) cc_final: 0.8038 (t) REVERT: E 321 SER cc_start: 0.7378 (p) cc_final: 0.7101 (t) REVERT: E 326 GLU cc_start: 0.6439 (mt-10) cc_final: 0.6153 (tt0) REVERT: E 356 ASP cc_start: 0.6967 (m-30) cc_final: 0.6604 (m-30) REVERT: E 373 LYS cc_start: 0.7876 (tttt) cc_final: 0.7594 (ttpt) REVERT: E 409 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7457 (ttpt) REVERT: E 412 PRO cc_start: 0.8707 (Cg_endo) cc_final: 0.8328 (Cg_exo) REVERT: E 474 ASN cc_start: 0.8002 (m-40) cc_final: 0.7733 (m-40) REVERT: E 486 PHE cc_start: 0.8021 (t80) cc_final: 0.7633 (t80) REVERT: E 502 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6747 (mt-10) REVERT: E 518 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.7847 (mtp-110) REVERT: E 521 MET cc_start: 0.7248 (mtp) cc_final: 0.6732 (mtp) REVERT: E 525 MET cc_start: 0.7347 (mmt) cc_final: 0.6924 (mmt) REVERT: E 527 PHE cc_start: 0.7030 (p90) cc_final: 0.6716 (p90) REVERT: E 530 SER cc_start: 0.8354 (t) cc_final: 0.7783 (p) REVERT: E 568 SER cc_start: 0.8132 (p) cc_final: 0.7872 (t) REVERT: E 577 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7676 (mtpp) REVERT: E 584 ASN cc_start: 0.7829 (t0) cc_final: 0.7612 (t0) REVERT: E 588 ILE cc_start: 0.8453 (mt) cc_final: 0.7999 (tt) REVERT: H 74 ARG cc_start: 0.7135 (mtt90) cc_final: 0.6752 (mtt-85) REVERT: H 76 THR cc_start: 0.7675 (m) cc_final: 0.7315 (p) REVERT: H 100 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6941 (mm-30) REVERT: H 111 LYS cc_start: 0.7840 (pttt) cc_final: 0.7358 (pttt) REVERT: H 124 GLN cc_start: 0.7191 (tm-30) cc_final: 0.6657 (tm-30) REVERT: H 130 SER cc_start: 0.8592 (t) cc_final: 0.8030 (p) REVERT: H 154 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6420 (mt-10) REVERT: H 173 ASP cc_start: 0.7429 (m-30) cc_final: 0.7161 (m-30) REVERT: H 212 MET cc_start: 0.7016 (mmm) cc_final: 0.6519 (mmm) REVERT: H 215 GLN cc_start: 0.7478 (mt0) cc_final: 0.7096 (mt0) REVERT: H 241 GLN cc_start: 0.8172 (pp30) cc_final: 0.7771 (pp30) REVERT: H 245 PHE cc_start: 0.7750 (m-80) cc_final: 0.6161 (m-80) REVERT: H 249 ASP cc_start: 0.6999 (m-30) cc_final: 0.6547 (m-30) REVERT: H 252 ARG cc_start: 0.7440 (ttm170) cc_final: 0.7156 (mtm-85) REVERT: H 254 ASN cc_start: 0.7995 (m-40) cc_final: 0.7727 (m-40) REVERT: H 256 MET cc_start: 0.7528 (ttp) cc_final: 0.7122 (ttp) REVERT: H 273 LYS cc_start: 0.7597 (tttt) cc_final: 0.7257 (tptt) REVERT: H 275 ASN cc_start: 0.7463 (p0) cc_final: 0.7258 (p0) REVERT: H 303 THR cc_start: 0.8348 (m) cc_final: 0.7609 (t) REVERT: H 314 PHE cc_start: 0.8445 (p90) cc_final: 0.8007 (p90) REVERT: H 315 MET cc_start: 0.7248 (mmm) cc_final: 0.6824 (mmm) REVERT: H 330 LEU cc_start: 0.8235 (tp) cc_final: 0.7736 (tt) REVERT: H 341 GLN cc_start: 0.8038 (tt0) cc_final: 0.7585 (tm-30) REVERT: H 350 MET cc_start: 0.7905 (ptp) cc_final: 0.7676 (ptp) REVERT: H 364 ARG cc_start: 0.7850 (ptp-170) cc_final: 0.7380 (ptm160) REVERT: H 381 GLN cc_start: 0.7265 (tp40) cc_final: 0.6718 (mm-40) REVERT: H 394 VAL cc_start: 0.8423 (t) cc_final: 0.8078 (m) REVERT: H 397 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6318 (mm-30) REVERT: H 404 LEU cc_start: 0.8510 (mp) cc_final: 0.8189 (mt) REVERT: H 409 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8695 (mttm) REVERT: H 463 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7084 (mt-10) REVERT: H 471 LEU cc_start: 0.8088 (tp) cc_final: 0.7783 (tp) REVERT: H 575 MET cc_start: 0.6813 (tpp) cc_final: 0.6483 (tpp) REVERT: H 593 PHE cc_start: 0.8050 (t80) cc_final: 0.7702 (t80) REVERT: H 594 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6449 (mm-30) outliers start: 57 outliers final: 41 residues processed: 653 average time/residue: 0.1252 time to fit residues: 119.7150 Evaluate side-chains 658 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 614 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 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 456 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain D residue 123 GLN 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 469 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain E residue 100 GLU 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 379 THR 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 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 107 CYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 496 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 161 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 399 GLN D 493 ASN E 236 ASN E 291 HIS H 136 HIS H 177 ASN H 190 ASN H 302 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.139925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121674 restraints weight = 26331.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.126216 restraints weight = 13298.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129214 restraints weight = 8106.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131162 restraints weight = 5550.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132523 restraints weight = 4148.289| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17320 Z= 0.155 Angle : 0.588 7.828 23497 Z= 0.310 Chirality : 0.044 0.205 2603 Planarity : 0.004 0.050 2976 Dihedral : 4.761 28.253 2177 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.27 % Allowed : 18.20 % Favored : 78.52 % 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: 0.23 (0.18), residues: 1978 helix: 1.48 (0.31), residues: 292 sheet: 0.50 (0.22), residues: 568 loop : -0.35 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 252 TYR 0.048 0.002 TYR E 214 PHE 0.026 0.002 PHE D 486 TRP 0.085 0.002 TRP H 567 HIS 0.008 0.001 HIS H 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (17259) covalent geometry : angle 0.57234 / 0.31 (23366) SS BOND : bond 0.00236 / 0.14 ( 16) SS BOND : angle 1.44319 / 0.87 ( 32) hydrogen bonds : bond 0.03969 / 2.59 ( 560) hydrogen bonds : angle 5.11894 / 3.52 ( 1413) metal coordination : bond 0.01037 / 0.63 ( 12) link_BETA1-4 : bond 0.00500 / 0.34 ( 11) link_BETA1-4 : angle 1.52169 / 0.93 ( 33) link_BETA1-6 : bond 0.00321 / 0.16 ( 4) link_BETA1-6 : angle 1.27786 / 0.75 ( 12) link_NAG-ASN : bond 0.00265 / 0.15 ( 18) link_NAG-ASN : angle 2.38878 / 1.80 ( 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 699 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 640 time to evaluate : 0.645 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: A 121 ILE cc_start: 0.7898 (tt) cc_final: 0.7298 (pt) REVERT: A 130 SER cc_start: 0.7452 (t) cc_final: 0.6496 (t) REVERT: A 141 ILE cc_start: 0.8113 (mt) cc_final: 0.7912 (mm) REVERT: A 150 LYS cc_start: 0.7759 (ttpp) cc_final: 0.6975 (ttpp) REVERT: A 153 ILE cc_start: 0.8102 (mt) cc_final: 0.7622 (tp) REVERT: A 154 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6730 (mt-10) REVERT: A 156 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6521 (mm-30) REVERT: A 269 CYS cc_start: 0.7181 (t) cc_final: 0.6965 (t) REVERT: A 293 ASP cc_start: 0.6601 (p0) cc_final: 0.6391 (t0) REVERT: A 362 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7716 (m) REVERT: A 372 ARG cc_start: 0.7213 (ttp-110) cc_final: 0.6874 (ptm-80) REVERT: A 376 LYS cc_start: 0.8085 (tttt) cc_final: 0.7645 (tttt) REVERT: A 428 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6494 (mt-10) REVERT: A 447 ASN cc_start: 0.7755 (m-40) cc_final: 0.7442 (m-40) REVERT: A 458 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7840 (ttp80) REVERT: A 521 MET cc_start: 0.7127 (mtp) cc_final: 0.6882 (mtp) REVERT: A 527 PHE cc_start: 0.7777 (p90) cc_final: 0.7208 (p90) REVERT: A 530 SER cc_start: 0.8345 (t) cc_final: 0.7893 (p) REVERT: A 583 LYS cc_start: 0.7834 (tptt) cc_final: 0.7370 (tptt) REVERT: A 585 ASP cc_start: 0.6614 (t0) cc_final: 0.6309 (t0) REVERT: D 45 GLU cc_start: 0.7864 (tt0) cc_final: 0.7341 (tt0) REVERT: D 79 ILE cc_start: 0.7458 (mm) cc_final: 0.7225 (mt) REVERT: D 85 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7163 (t0) REVERT: D 101 MET cc_start: 0.7089 (mmm) cc_final: 0.6685 (mmm) REVERT: D 105 LYS cc_start: 0.8023 (mttt) cc_final: 0.7749 (mttt) REVERT: D 123 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6203 (mm110) REVERT: D 125 PHE cc_start: 0.7213 (m-10) cc_final: 0.6458 (m-10) REVERT: D 134 ASP cc_start: 0.6571 (p0) cc_final: 0.6169 (p0) REVERT: D 135 GLN cc_start: 0.7289 (mm110) cc_final: 0.6894 (mm110) REVERT: D 141 ILE cc_start: 0.7736 (mt) cc_final: 0.7467 (mm) REVERT: D 142 SER cc_start: 0.8065 (t) cc_final: 0.7223 (p) REVERT: D 156 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6365 (mm-30) REVERT: D 241 GLN cc_start: 0.7600 (pp30) cc_final: 0.7195 (pp30) REVERT: D 244 ASP cc_start: 0.7123 (t70) cc_final: 0.6580 (t70) REVERT: D 270 THR cc_start: 0.7347 (p) cc_final: 0.7047 (t) REVERT: D 287 THR cc_start: 0.7387 (t) cc_final: 0.6980 (m) REVERT: D 315 MET cc_start: 0.6334 (mmm) cc_final: 0.5884 (mmm) REVERT: D 330 LEU cc_start: 0.7552 (mt) cc_final: 0.6958 (mt) REVERT: D 342 GLN cc_start: 0.8098 (mp10) cc_final: 0.7350 (mp10) REVERT: D 345 GLN cc_start: 0.7897 (tt0) cc_final: 0.7463 (tt0) REVERT: D 362 VAL cc_start: 0.7967 (t) cc_final: 0.7707 (p) REVERT: D 374 LEU cc_start: 0.8493 (mt) cc_final: 0.8229 (mt) REVERT: D 389 LYS cc_start: 0.8126 (mttm) cc_final: 0.7798 (mttp) REVERT: D 404 LEU cc_start: 0.7778 (mp) cc_final: 0.7460 (mt) REVERT: D 405 PHE cc_start: 0.7638 (m-10) cc_final: 0.7283 (m-80) REVERT: D 428 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6481 (mt-10) REVERT: D 445 LEU cc_start: 0.8289 (tp) cc_final: 0.8081 (mt) REVERT: D 453 LYS cc_start: 0.7158 (pttt) cc_final: 0.6638 (pttt) REVERT: D 455 GLN cc_start: 0.7560 (mp10) cc_final: 0.6947 (mp-120) REVERT: D 486 PHE cc_start: 0.7916 (t80) cc_final: 0.7715 (t80) REVERT: D 512 ASP cc_start: 0.7141 (t0) cc_final: 0.6847 (t0) REVERT: D 544 TRP cc_start: 0.8100 (m100) cc_final: 0.7655 (m100) REVERT: D 573 HIS cc_start: 0.7267 (m170) cc_final: 0.6755 (m170) REVERT: D 577 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7342 (mmtt) REVERT: D 588 ILE cc_start: 0.8641 (mt) cc_final: 0.8352 (mm) REVERT: D 599 LEU cc_start: 0.7912 (mt) cc_final: 0.7684 (mt) REVERT: E 76 THR cc_start: 0.7676 (m) cc_final: 0.7456 (p) REVERT: E 100 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: E 131 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6526 (mt-10) REVERT: E 135 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7328 (mm110) REVERT: E 136 HIS cc_start: 0.7501 (m-70) cc_final: 0.7069 (m-70) REVERT: E 143 ILE cc_start: 0.8337 (mm) cc_final: 0.8041 (tp) REVERT: E 180 TRP cc_start: 0.8266 (m100) cc_final: 0.8032 (m100) REVERT: E 209 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6753 (mm-30) REVERT: E 224 SER cc_start: 0.7386 (m) cc_final: 0.6938 (p) REVERT: E 234 GLU cc_start: 0.7488 (mp0) cc_final: 0.7200 (mp0) REVERT: E 241 GLN cc_start: 0.8244 (pp30) cc_final: 0.7812 (pp30) REVERT: E 251 GLU cc_start: 0.7284 (tp30) cc_final: 0.6511 (tp30) REVERT: E 256 MET cc_start: 0.7147 (ttp) cc_final: 0.6721 (ttp) REVERT: E 266 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7960 (mm) REVERT: E 299 GLU cc_start: 0.6645 (mt-10) cc_final: 0.6143 (mt-10) REVERT: E 303 THR cc_start: 0.8374 (m) cc_final: 0.7876 (t) REVERT: E 315 MET cc_start: 0.7261 (mmm) cc_final: 0.6456 (mmm) REVERT: E 321 SER cc_start: 0.7435 (p) cc_final: 0.7121 (t) REVERT: E 326 GLU cc_start: 0.6472 (mt-10) cc_final: 0.6143 (tt0) REVERT: E 329 LEU cc_start: 0.7763 (mt) cc_final: 0.7560 (tp) REVERT: E 356 ASP cc_start: 0.6896 (m-30) cc_final: 0.6570 (m-30) REVERT: E 373 LYS cc_start: 0.7893 (tttt) cc_final: 0.7588 (ttpt) REVERT: E 384 ASP cc_start: 0.6935 (m-30) cc_final: 0.6637 (m-30) REVERT: E 409 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7622 (ttpp) REVERT: E 412 PRO cc_start: 0.8714 (Cg_endo) cc_final: 0.8374 (Cg_exo) REVERT: E 474 ASN cc_start: 0.7980 (m-40) cc_final: 0.7758 (m-40) REVERT: E 486 PHE cc_start: 0.8060 (t80) cc_final: 0.7645 (t80) REVERT: E 493 ASN cc_start: 0.7847 (m-40) cc_final: 0.7571 (m110) REVERT: E 502 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6667 (mt-10) REVERT: E 518 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.7871 (mtp-110) REVERT: E 521 MET cc_start: 0.7193 (mtp) cc_final: 0.6701 (mtp) REVERT: E 525 MET cc_start: 0.7358 (mmt) cc_final: 0.6945 (mmt) REVERT: E 527 PHE cc_start: 0.7122 (p90) cc_final: 0.6793 (p90) REVERT: E 530 SER cc_start: 0.8420 (t) cc_final: 0.7872 (p) REVERT: E 568 SER cc_start: 0.8125 (p) cc_final: 0.7872 (t) REVERT: E 577 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7684 (mtpp) REVERT: E 584 ASN cc_start: 0.7813 (t0) cc_final: 0.7569 (t0) REVERT: E 588 ILE cc_start: 0.8433 (mt) cc_final: 0.7985 (tt) REVERT: H 74 ARG cc_start: 0.7140 (mtt90) cc_final: 0.6752 (mtt-85) REVERT: H 76 THR cc_start: 0.7679 (m) cc_final: 0.7325 (p) REVERT: H 111 LYS cc_start: 0.7860 (pttt) cc_final: 0.7386 (pttt) REVERT: H 124 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6974 (tm-30) REVERT: H 154 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6692 (mt-10) REVERT: H 173 ASP cc_start: 0.7441 (m-30) cc_final: 0.7186 (m-30) REVERT: H 212 MET cc_start: 0.7055 (mmm) cc_final: 0.6595 (mmm) REVERT: H 215 GLN cc_start: 0.7507 (mt0) cc_final: 0.7135 (mt0) REVERT: H 217 PHE cc_start: 0.8324 (m-80) cc_final: 0.7803 (m-80) REVERT: H 241 GLN cc_start: 0.8254 (pp30) cc_final: 0.7949 (pp30) REVERT: H 249 ASP cc_start: 0.6954 (m-30) cc_final: 0.6541 (m-30) REVERT: H 254 ASN cc_start: 0.7971 (m-40) cc_final: 0.7702 (m-40) REVERT: H 256 MET cc_start: 0.7562 (ttp) cc_final: 0.7192 (ttp) REVERT: H 273 LYS cc_start: 0.7598 (tttt) cc_final: 0.7259 (tptt) REVERT: H 275 ASN cc_start: 0.7478 (p0) cc_final: 0.7242 (p0) REVERT: H 303 THR cc_start: 0.8343 (m) cc_final: 0.7577 (t) REVERT: H 314 PHE cc_start: 0.8456 (p90) cc_final: 0.8057 (p90) REVERT: H 315 MET cc_start: 0.7255 (mmm) cc_final: 0.6818 (mmm) REVERT: H 326 GLU cc_start: 0.6478 (mt-10) cc_final: 0.6267 (mt-10) REVERT: H 330 LEU cc_start: 0.8222 (tp) cc_final: 0.7850 (tt) REVERT: H 341 GLN cc_start: 0.8043 (tt0) cc_final: 0.7610 (tm-30) REVERT: H 364 ARG cc_start: 0.7870 (ptp-170) cc_final: 0.7170 (ptm160) REVERT: H 373 LYS cc_start: 0.7936 (ttpp) cc_final: 0.7356 (ttpp) REVERT: H 381 GLN cc_start: 0.7333 (tp40) cc_final: 0.6754 (mm-40) REVERT: H 394 VAL cc_start: 0.8326 (t) cc_final: 0.7954 (m) REVERT: H 397 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6327 (mm-30) REVERT: H 404 LEU cc_start: 0.8482 (mp) cc_final: 0.8151 (mt) REVERT: H 463 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7116 (mt-10) REVERT: H 471 LEU cc_start: 0.8110 (tp) cc_final: 0.7813 (tp) REVERT: H 502 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6994 (mm-30) REVERT: H 521 MET cc_start: 0.7436 (mtp) cc_final: 0.6918 (mtp) REVERT: H 575 MET cc_start: 0.6799 (tpp) cc_final: 0.6455 (tpp) REVERT: H 584 ASN cc_start: 0.7906 (t0) cc_final: 0.7554 (t0) REVERT: H 593 PHE cc_start: 0.8071 (t80) cc_final: 0.7584 (t80) REVERT: H 594 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6424 (mm-30) outliers start: 59 outliers final: 46 residues processed: 667 average time/residue: 0.1314 time to fit residues: 127.8703 Evaluate side-chains 655 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 603 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 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 400 LYS Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 582 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 398 GLU Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 132 VAL 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 266 LEU 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 421 LEU 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 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 107 CYS Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 372 ARG Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 455 GLN Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain H residue 502 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 117 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 158 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 HIS A 316 GLN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN D 302 HIS D 341 GLN D 505 GLN E 236 ASN H 136 HIS H 190 ASN H 302 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122431 restraints weight = 26223.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.126920 restraints weight = 13137.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129911 restraints weight = 7977.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131843 restraints weight = 5453.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133216 restraints weight = 4057.065| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17320 Z= 0.161 Angle : 0.601 7.782 23497 Z= 0.317 Chirality : 0.044 0.203 2603 Planarity : 0.004 0.047 2976 Dihedral : 4.790 27.990 2177 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.05 % Allowed : 19.87 % Favored : 77.08 % 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: 0.16 (0.18), residues: 1978 helix: 1.47 (0.30), residues: 293 sheet: 0.43 (0.22), residues: 573 loop : -0.40 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 74 TYR 0.034 0.002 TYR E 214 PHE 0.030 0.002 PHE E 55 TRP 0.104 0.002 TRP H 567 HIS 0.008 0.001 HIS D 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (17259) covalent geometry : angle 0.58604 / 0.31 (23366) SS BOND : bond 0.00271 / 0.15 ( 16) SS BOND : angle 1.47367 / 0.86 ( 32) hydrogen bonds : bond 0.03942 / 2.57 ( 560) hydrogen bonds : angle 5.13254 / 3.52 ( 1413) metal coordination : bond 0.01153 / 0.67 ( 12) link_BETA1-4 : bond 0.00533 / 0.35 ( 11) link_BETA1-4 : angle 1.52142 / 0.93 ( 33) link_BETA1-6 : bond 0.00298 / 0.15 ( 4) link_BETA1-6 : angle 1.26010 / 0.75 ( 12) link_NAG-ASN : bond 0.00268 / 0.15 ( 18) link_NAG-ASN : angle 2.37154 / 1.79 ( 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 670 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 615 time to evaluate : 0.562 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: 0.7904 (tt) cc_final: 0.7295 (pt) REVERT: A 130 SER cc_start: 0.7461 (t) cc_final: 0.6548 (t) REVERT: A 141 ILE cc_start: 0.8130 (mt) cc_final: 0.7908 (mm) REVERT: A 150 LYS cc_start: 0.7853 (ttpp) cc_final: 0.6980 (ttpp) REVERT: A 153 ILE cc_start: 0.8110 (mt) cc_final: 0.7634 (tp) REVERT: A 154 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6856 (mt-10) REVERT: A 156 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6543 (mm-30) REVERT: A 293 ASP cc_start: 0.6650 (p0) cc_final: 0.6448 (t0) REVERT: A 372 ARG cc_start: 0.7199 (ttp-110) cc_final: 0.6836 (ptm-80) REVERT: A 375 VAL cc_start: 0.8117 (t) cc_final: 0.7777 (p) REVERT: A 376 LYS cc_start: 0.8088 (tttt) cc_final: 0.7758 (tttt) REVERT: A 428 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6512 (mt-10) REVERT: A 438 VAL cc_start: 0.8265 (t) cc_final: 0.7841 (p) REVERT: A 447 ASN cc_start: 0.7791 (m-40) cc_final: 0.7499 (m-40) REVERT: A 458 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7849 (ttp80) REVERT: A 521 MET cc_start: 0.7169 (mtp) cc_final: 0.6956 (mtp) REVERT: A 527 PHE cc_start: 0.7740 (p90) cc_final: 0.7212 (p90) REVERT: A 530 SER cc_start: 0.8382 (t) cc_final: 0.7893 (p) REVERT: A 583 LYS cc_start: 0.7909 (tptt) cc_final: 0.7598 (tptt) REVERT: A 585 ASP cc_start: 0.6672 (t0) cc_final: 0.6344 (t0) REVERT: D 45 GLU cc_start: 0.7837 (tt0) cc_final: 0.7317 (tt0) REVERT: D 79 ILE cc_start: 0.7489 (mm) cc_final: 0.7282 (mp) REVERT: D 85 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7159 (t0) REVERT: D 101 MET cc_start: 0.7089 (mmm) cc_final: 0.6663 (mmm) REVERT: D 105 LYS cc_start: 0.8000 (mttt) cc_final: 0.7571 (mtmt) REVERT: D 135 GLN cc_start: 0.7278 (mm110) cc_final: 0.6838 (mm110) REVERT: D 141 ILE cc_start: 0.7745 (mt) cc_final: 0.7396 (mm) REVERT: D 156 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6424 (mm-30) REVERT: D 242 ARG cc_start: 0.7402 (mmt90) cc_final: 0.7102 (mmt-90) REVERT: D 244 ASP cc_start: 0.7114 (t70) cc_final: 0.6372 (t70) REVERT: D 270 THR cc_start: 0.7308 (p) cc_final: 0.7064 (t) REVERT: D 287 THR cc_start: 0.7374 (t) cc_final: 0.7037 (m) REVERT: D 301 ASP cc_start: 0.7055 (p0) cc_final: 0.6830 (p0) REVERT: D 315 MET cc_start: 0.6317 (mmm) cc_final: 0.5874 (mmm) REVERT: D 330 LEU cc_start: 0.7532 (mt) cc_final: 0.6940 (mt) REVERT: D 345 GLN cc_start: 0.7919 (tt0) cc_final: 0.7435 (tt0) REVERT: D 362 VAL cc_start: 0.8033 (t) cc_final: 0.7773 (p) REVERT: D 374 LEU cc_start: 0.8463 (mt) cc_final: 0.8228 (mt) REVERT: D 389 LYS cc_start: 0.8150 (mttm) cc_final: 0.7815 (mttp) REVERT: D 402 ARG cc_start: 0.6844 (mtt-85) cc_final: 0.6555 (mtt-85) REVERT: D 404 LEU cc_start: 0.7804 (mp) cc_final: 0.7530 (mt) REVERT: D 405 PHE cc_start: 0.7652 (m-10) cc_final: 0.7313 (m-80) REVERT: D 428 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6479 (mt-10) REVERT: D 445 LEU cc_start: 0.8323 (tp) cc_final: 0.8115 (mt) REVERT: D 453 LYS cc_start: 0.7244 (pttt) cc_final: 0.6490 (pttt) REVERT: D 455 GLN cc_start: 0.7534 (mp10) cc_final: 0.6866 (mp10) REVERT: D 486 PHE cc_start: 0.7959 (t80) cc_final: 0.7739 (t80) REVERT: D 512 ASP cc_start: 0.7113 (t0) cc_final: 0.6789 (t0) REVERT: D 544 TRP cc_start: 0.8116 (m100) cc_final: 0.7721 (m100) REVERT: D 573 HIS cc_start: 0.7325 (m170) cc_final: 0.6830 (m170) REVERT: D 577 LYS cc_start: 0.7726 (mmtt) cc_final: 0.7339 (mmtt) REVERT: D 588 ILE cc_start: 0.8602 (mt) cc_final: 0.8342 (mm) REVERT: D 599 LEU cc_start: 0.7938 (mt) cc_final: 0.7670 (mt) REVERT: E 76 THR cc_start: 0.7676 (m) cc_final: 0.7435 (p) REVERT: E 100 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: E 126 ASP cc_start: 0.8022 (m-30) cc_final: 0.7551 (m-30) REVERT: E 131 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6551 (mt-10) REVERT: E 136 HIS cc_start: 0.7475 (m-70) cc_final: 0.7001 (m-70) REVERT: E 143 ILE cc_start: 0.8325 (mm) cc_final: 0.8007 (tp) REVERT: E 180 TRP cc_start: 0.8288 (m100) cc_final: 0.8071 (m100) REVERT: E 209 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6752 (mm-30) REVERT: E 212 MET cc_start: 0.6620 (mmm) cc_final: 0.6196 (mmm) REVERT: E 224 SER cc_start: 0.7344 (m) cc_final: 0.7010 (p) REVERT: E 241 GLN cc_start: 0.8262 (pp30) cc_final: 0.7836 (pp30) REVERT: E 251 GLU cc_start: 0.7263 (tp30) cc_final: 0.6490 (tp30) REVERT: E 256 MET cc_start: 0.7019 (ttp) cc_final: 0.6739 (ttp) REVERT: E 266 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7971 (mm) REVERT: E 299 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6172 (mt-10) REVERT: E 303 THR cc_start: 0.8299 (m) cc_final: 0.7809 (t) REVERT: E 315 MET cc_start: 0.7238 (mmm) cc_final: 0.6433 (mmm) REVERT: E 326 GLU cc_start: 0.6501 (mt-10) cc_final: 0.6215 (tt0) REVERT: E 338 LYS cc_start: 0.8111 (mttt) cc_final: 0.7870 (mtmt) REVERT: E 350 MET cc_start: 0.7346 (mtm) cc_final: 0.6877 (ptm) REVERT: E 356 ASP cc_start: 0.6863 (m-30) cc_final: 0.6569 (m-30) REVERT: E 373 LYS cc_start: 0.7937 (tttt) cc_final: 0.7640 (ttmm) REVERT: E 474 ASN cc_start: 0.7999 (m-40) cc_final: 0.7794 (m-40) REVERT: E 486 PHE cc_start: 0.8081 (t80) cc_final: 0.7691 (t80) REVERT: E 493 ASN cc_start: 0.7849 (m-40) cc_final: 0.7597 (m110) REVERT: E 502 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6672 (mt-10) REVERT: E 518 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7790 (mtp-110) REVERT: E 521 MET cc_start: 0.7108 (mtp) cc_final: 0.6522 (mtp) REVERT: E 525 MET cc_start: 0.7344 (mmt) cc_final: 0.6901 (mmt) REVERT: E 527 PHE cc_start: 0.7117 (p90) cc_final: 0.6769 (p90) REVERT: E 530 SER cc_start: 0.8446 (t) cc_final: 0.7921 (p) REVERT: E 568 SER cc_start: 0.8146 (p) cc_final: 0.7919 (t) REVERT: E 584 ASN cc_start: 0.7738 (t0) cc_final: 0.7475 (t0) REVERT: E 588 ILE cc_start: 0.8452 (mt) cc_final: 0.8010 (tt) REVERT: H 74 ARG cc_start: 0.7126 (mtt90) cc_final: 0.6586 (mtt-85) REVERT: H 76 THR cc_start: 0.7674 (m) cc_final: 0.7322 (p) REVERT: H 111 LYS cc_start: 0.7865 (pttt) cc_final: 0.7395 (pttt) REVERT: H 124 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6979 (tm-30) REVERT: H 154 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6691 (mt-10) REVERT: H 173 ASP cc_start: 0.7425 (m-30) cc_final: 0.7180 (m-30) REVERT: H 212 MET cc_start: 0.7033 (mmm) cc_final: 0.6574 (mmm) REVERT: H 215 GLN cc_start: 0.7534 (mt0) cc_final: 0.7195 (mt0) REVERT: H 241 GLN cc_start: 0.8220 (pp30) cc_final: 0.7900 (pp30) REVERT: H 249 ASP cc_start: 0.6954 (m-30) cc_final: 0.6586 (m-30) REVERT: H 254 ASN cc_start: 0.7943 (m-40) cc_final: 0.7689 (m-40) REVERT: H 256 MET cc_start: 0.7584 (ttp) cc_final: 0.6526 (ttp) REVERT: H 273 LYS cc_start: 0.7596 (tttt) cc_final: 0.7273 (tptt) REVERT: H 275 ASN cc_start: 0.7487 (p0) cc_final: 0.7267 (p0) REVERT: H 303 THR cc_start: 0.8344 (m) cc_final: 0.7568 (t) REVERT: H 314 PHE cc_start: 0.8458 (p90) cc_final: 0.8057 (p90) REVERT: H 315 MET cc_start: 0.7241 (mmm) cc_final: 0.6822 (mmm) REVERT: H 330 LEU cc_start: 0.8161 (tp) cc_final: 0.7827 (tt) REVERT: H 341 GLN cc_start: 0.8033 (tt0) cc_final: 0.7575 (tm-30) REVERT: H 362 VAL cc_start: 0.8384 (t) cc_final: 0.8048 (p) REVERT: H 364 ARG cc_start: 0.7832 (ptp-170) cc_final: 0.7112 (ptm160) REVERT: H 373 LYS cc_start: 0.7925 (ttpp) cc_final: 0.7338 (ttpp) REVERT: H 381 GLN cc_start: 0.7391 (tp40) cc_final: 0.7172 (mm-40) REVERT: H 394 VAL cc_start: 0.8359 (t) cc_final: 0.7975 (m) REVERT: H 397 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6339 (mm-30) REVERT: H 404 LEU cc_start: 0.8488 (mp) cc_final: 0.8181 (mt) REVERT: H 409 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8579 (mttm) REVERT: H 463 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7105 (mt-10) REVERT: H 471 LEU cc_start: 0.8134 (tp) cc_final: 0.7863 (tp) REVERT: H 502 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6912 (mm-30) REVERT: H 521 MET cc_start: 0.7485 (mtp) cc_final: 0.6919 (mtp) REVERT: H 543 ILE cc_start: 0.7862 (mt) cc_final: 0.7660 (mt) REVERT: H 575 MET cc_start: 0.6807 (tpp) cc_final: 0.6408 (tpp) REVERT: H 584 ASN cc_start: 0.7895 (t0) cc_final: 0.7561 (t0) REVERT: H 593 PHE cc_start: 0.8080 (t80) cc_final: 0.7614 (t80) REVERT: H 594 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6471 (mm-30) outliers start: 55 outliers final: 45 residues processed: 638 average time/residue: 0.1287 time to fit residues: 120.4974 Evaluate side-chains 651 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 602 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 220 ASN Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain D residue 85 ASP 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 469 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 139 GLN 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 266 LEU Chi-restraints excluded: chain E residue 280 ILE 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 404 LEU 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 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 107 CYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 372 ARG Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 455 GLN Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain H residue 502 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 127 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 199 optimal weight: 0.0470 chunk 57 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 10 optimal weight: 0.0030 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS A 302 HIS A 387 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 HIS ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN H 136 HIS H 177 ASN H 190 ASN H 302 HIS H 386 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123234 restraints weight = 26204.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127803 restraints weight = 13157.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130805 restraints weight = 7987.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132738 restraints weight = 5452.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134122 restraints weight = 4067.298| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17320 Z= 0.109 Angle : 0.578 8.465 23497 Z= 0.303 Chirality : 0.043 0.210 2603 Planarity : 0.004 0.046 2976 Dihedral : 4.633 26.291 2177 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.61 % Allowed : 21.14 % Favored : 76.25 % 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: 0.27 (0.19), residues: 1978 helix: 1.58 (0.31), residues: 293 sheet: 0.43 (0.22), residues: 564 loop : -0.28 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 549 TYR 0.040 0.001 TYR E 214 PHE 0.030 0.002 PHE E 55 TRP 0.094 0.002 TRP H 567 HIS 0.009 0.001 HIS D 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (17259) covalent geometry : angle 0.56486 / 0.30 (23366) SS BOND : bond 0.00201 / 0.11 ( 16) SS BOND : angle 1.25045 / 0.73 ( 32) hydrogen bonds : bond 0.03410 / 2.22 ( 560) hydrogen bonds : angle 5.13052 / 3.52 ( 1413) metal coordination : bond 0.00491 / 0.29 ( 12) link_BETA1-4 : bond 0.00446 / 0.30 ( 11) link_BETA1-4 : angle 1.44296 / 0.88 ( 33) link_BETA1-6 : bond 0.00353 / 0.18 ( 4) link_BETA1-6 : angle 1.21931 / 0.73 ( 12) link_NAG-ASN : bond 0.00146 / 0.08 ( 18) link_NAG-ASN : angle 2.16081 / 1.63 ( 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 667 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 620 time to evaluate : 0.550 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 120 ILE cc_start: 0.8373 (mt) cc_final: 0.7980 (pt) REVERT: A 121 ILE cc_start: 0.7918 (tt) cc_final: 0.7290 (pt) REVERT: A 130 SER cc_start: 0.7407 (t) cc_final: 0.6649 (t) REVERT: A 141 ILE cc_start: 0.8066 (mt) cc_final: 0.7799 (mm) REVERT: A 150 LYS cc_start: 0.7648 (ttpp) cc_final: 0.6777 (ttpp) REVERT: A 153 ILE cc_start: 0.8054 (mt) cc_final: 0.7584 (tp) REVERT: A 154 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6767 (mt-10) REVERT: A 156 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6513 (mm-30) REVERT: A 293 ASP cc_start: 0.6563 (p0) cc_final: 0.6359 (t0) REVERT: A 375 VAL cc_start: 0.8109 (t) cc_final: 0.7769 (p) REVERT: A 428 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6506 (mt-10) REVERT: A 447 ASN cc_start: 0.7785 (m-40) cc_final: 0.7488 (m-40) REVERT: A 521 MET cc_start: 0.7127 (mtp) cc_final: 0.6905 (mtp) REVERT: A 527 PHE cc_start: 0.7708 (p90) cc_final: 0.7115 (p90) REVERT: A 583 LYS cc_start: 0.7879 (tptt) cc_final: 0.7538 (tptt) REVERT: A 585 ASP cc_start: 0.6677 (t0) cc_final: 0.6248 (t0) REVERT: D 45 GLU cc_start: 0.7811 (tt0) cc_final: 0.7284 (tt0) REVERT: D 85 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7090 (t0) REVERT: D 101 MET cc_start: 0.7118 (mmm) cc_final: 0.6723 (mmm) REVERT: D 105 LYS cc_start: 0.7930 (mttt) cc_final: 0.7706 (mttt) REVERT: D 135 GLN cc_start: 0.7292 (mm110) cc_final: 0.6790 (mm110) REVERT: D 141 ILE cc_start: 0.7740 (mt) cc_final: 0.7402 (mm) REVERT: D 156 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6445 (mm-30) REVERT: D 241 GLN cc_start: 0.7712 (pp30) cc_final: 0.7172 (pp30) REVERT: D 244 ASP cc_start: 0.7102 (t70) cc_final: 0.6577 (t70) REVERT: D 270 THR cc_start: 0.7258 (p) cc_final: 0.7015 (t) REVERT: D 287 THR cc_start: 0.7382 (t) cc_final: 0.7013 (m) REVERT: D 301 ASP cc_start: 0.7060 (p0) cc_final: 0.6834 (p0) REVERT: D 315 MET cc_start: 0.6324 (mmm) cc_final: 0.5890 (mmm) REVERT: D 316 GLN cc_start: 0.6760 (tm-30) cc_final: 0.6460 (tm-30) REVERT: D 330 LEU cc_start: 0.7562 (mt) cc_final: 0.6962 (mt) REVERT: D 342 GLN cc_start: 0.8093 (mp10) cc_final: 0.7340 (mp10) REVERT: D 345 GLN cc_start: 0.7889 (tt0) cc_final: 0.7408 (tt0) REVERT: D 362 VAL cc_start: 0.7993 (t) cc_final: 0.7702 (p) REVERT: D 374 LEU cc_start: 0.8466 (mt) cc_final: 0.8203 (mt) REVERT: D 389 LYS cc_start: 0.8172 (mttm) cc_final: 0.7837 (mttp) REVERT: D 402 ARG cc_start: 0.6804 (mtt-85) cc_final: 0.6552 (mtt-85) REVERT: D 405 PHE cc_start: 0.7631 (m-10) cc_final: 0.7297 (m-80) REVERT: D 428 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6467 (mt-10) REVERT: D 444 VAL cc_start: 0.8268 (t) cc_final: 0.8065 (p) REVERT: D 445 LEU cc_start: 0.8406 (tp) cc_final: 0.8109 (mt) REVERT: D 453 LYS cc_start: 0.7186 (pttt) cc_final: 0.6607 (pttt) REVERT: D 455 GLN cc_start: 0.7511 (mp10) cc_final: 0.6879 (mp-120) REVERT: D 504 ARG cc_start: 0.7459 (mpt180) cc_final: 0.7005 (mpt180) REVERT: D 512 ASP cc_start: 0.7083 (t0) cc_final: 0.6763 (t0) REVERT: D 544 TRP cc_start: 0.8115 (m100) cc_final: 0.7686 (m100) REVERT: D 573 HIS cc_start: 0.7299 (m170) cc_final: 0.6818 (m170) REVERT: D 577 LYS cc_start: 0.7712 (mmtt) cc_final: 0.7351 (mmtt) REVERT: D 599 LEU cc_start: 0.7918 (mt) cc_final: 0.7645 (mt) REVERT: E 76 THR cc_start: 0.7663 (m) cc_final: 0.7416 (p) REVERT: E 100 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7016 (tm-30) REVERT: E 131 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6469 (mt-10) REVERT: E 136 HIS cc_start: 0.7447 (m-70) cc_final: 0.7030 (m-70) REVERT: E 143 ILE cc_start: 0.8234 (mm) cc_final: 0.7897 (tp) REVERT: E 180 TRP cc_start: 0.8295 (m100) cc_final: 0.8048 (m100) REVERT: E 209 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6767 (mm-30) REVERT: E 212 MET cc_start: 0.6551 (mmm) cc_final: 0.6149 (mmm) REVERT: E 224 SER cc_start: 0.7437 (m) cc_final: 0.7068 (p) REVERT: E 241 GLN cc_start: 0.8284 (pp30) cc_final: 0.7882 (pp30) REVERT: E 249 ASP cc_start: 0.7017 (m-30) cc_final: 0.6724 (m-30) REVERT: E 256 MET cc_start: 0.6896 (ttp) cc_final: 0.6513 (ttp) REVERT: E 266 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7912 (mm) REVERT: E 287 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7917 (m) REVERT: E 299 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6113 (mt-10) REVERT: E 301 ASP cc_start: 0.7798 (p0) cc_final: 0.7508 (p0) REVERT: E 303 THR cc_start: 0.8302 (m) cc_final: 0.8009 (m) REVERT: E 315 MET cc_start: 0.7336 (mmm) cc_final: 0.6783 (mmm) REVERT: E 338 LYS cc_start: 0.8096 (mttt) cc_final: 0.7829 (mptt) REVERT: E 350 MET cc_start: 0.7313 (mtm) cc_final: 0.6888 (ptm) REVERT: E 356 ASP cc_start: 0.6796 (m-30) cc_final: 0.6562 (m-30) REVERT: E 373 LYS cc_start: 0.7915 (tttt) cc_final: 0.7580 (ttpt) REVERT: E 381 GLN cc_start: 0.7569 (tp40) cc_final: 0.7096 (mm-40) REVERT: E 409 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7649 (ttpt) REVERT: E 486 PHE cc_start: 0.8037 (t80) cc_final: 0.7646 (t80) REVERT: E 502 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6673 (mt-10) REVERT: E 518 ARG cc_start: 0.8262 (ttp-110) cc_final: 0.7923 (mtp-110) REVERT: E 521 MET cc_start: 0.7097 (mtp) cc_final: 0.6510 (mtp) REVERT: E 525 MET cc_start: 0.7326 (mmt) cc_final: 0.6900 (mmt) REVERT: E 527 PHE cc_start: 0.7082 (p90) cc_final: 0.6756 (p90) REVERT: E 530 SER cc_start: 0.8432 (t) cc_final: 0.7896 (p) REVERT: E 568 SER cc_start: 0.8156 (p) cc_final: 0.7919 (t) REVERT: E 577 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7676 (mtpp) REVERT: E 588 ILE cc_start: 0.8428 (mt) cc_final: 0.7998 (tt) REVERT: H 74 ARG cc_start: 0.7114 (mtt90) cc_final: 0.6600 (mtt-85) REVERT: H 76 THR cc_start: 0.7665 (m) cc_final: 0.7308 (p) REVERT: H 111 LYS cc_start: 0.7865 (pttt) cc_final: 0.7385 (pttt) REVERT: H 124 GLN cc_start: 0.7203 (tm-30) cc_final: 0.6959 (tm-30) REVERT: H 130 SER cc_start: 0.8671 (t) cc_final: 0.8097 (p) REVERT: H 154 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6625 (mt-10) REVERT: H 166 GLU cc_start: 0.7318 (tp30) cc_final: 0.6884 (tp30) REVERT: H 173 ASP cc_start: 0.7404 (m-30) cc_final: 0.7148 (m-30) REVERT: H 212 MET cc_start: 0.6995 (mmm) cc_final: 0.6516 (mmm) REVERT: H 215 GLN cc_start: 0.7621 (mt0) cc_final: 0.7248 (mt0) REVERT: H 241 GLN cc_start: 0.8212 (pp30) cc_final: 0.7905 (pp30) REVERT: H 249 ASP cc_start: 0.6934 (m-30) cc_final: 0.6546 (m-30) REVERT: H 254 ASN cc_start: 0.7899 (m-40) cc_final: 0.7625 (m-40) REVERT: H 256 MET cc_start: 0.7559 (ttp) cc_final: 0.6623 (ttp) REVERT: H 273 LYS cc_start: 0.7574 (tttt) cc_final: 0.7260 (tptt) REVERT: H 314 PHE cc_start: 0.8442 (p90) cc_final: 0.8103 (p90) REVERT: H 330 LEU cc_start: 0.8161 (tp) cc_final: 0.7803 (tt) REVERT: H 341 GLN cc_start: 0.7987 (tt0) cc_final: 0.7522 (tm-30) REVERT: H 362 VAL cc_start: 0.8351 (t) cc_final: 0.7983 (p) REVERT: H 364 ARG cc_start: 0.7811 (ptp-170) cc_final: 0.7094 (ptm160) REVERT: H 373 LYS cc_start: 0.7981 (ttpp) cc_final: 0.7394 (ttpp) REVERT: H 381 GLN cc_start: 0.7373 (tp40) cc_final: 0.7149 (mm-40) REVERT: H 394 VAL cc_start: 0.8306 (t) cc_final: 0.8081 (m) REVERT: H 397 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6288 (mm-30) REVERT: H 404 LEU cc_start: 0.8480 (mp) cc_final: 0.8168 (mt) REVERT: H 409 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8526 (mttm) REVERT: H 463 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7090 (mt-10) REVERT: H 502 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6905 (mm-30) REVERT: H 521 MET cc_start: 0.7450 (mtp) cc_final: 0.6890 (mtp) REVERT: H 575 MET cc_start: 0.6789 (tpp) cc_final: 0.6364 (tpp) REVERT: H 593 PHE cc_start: 0.8132 (t80) cc_final: 0.7614 (t80) REVERT: H 594 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6396 (mm-30) outliers start: 47 outliers final: 39 residues processed: 642 average time/residue: 0.1308 time to fit residues: 122.5212 Evaluate side-chains 638 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 594 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 263 HIS Chi-restraints excluded: chain A residue 269 CYS 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 493 ASN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 339 ARG Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 185 SER 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 331 GLU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 497 LEU 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 H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 455 GLN Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain H residue 502 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 157 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 98 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 HIS ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN D 302 HIS D 399 GLN D 505 GLN E 487 HIS H 136 HIS H 190 ASN H 302 HIS H 341 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.140287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.123225 restraints weight = 26589.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127313 restraints weight = 14140.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.130023 restraints weight = 8930.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131824 restraints weight = 6269.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133049 restraints weight = 4785.769| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17320 Z= 0.183 Angle : 0.622 8.085 23497 Z= 0.327 Chirality : 0.045 0.302 2603 Planarity : 0.004 0.048 2976 Dihedral : 4.887 46.465 2177 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.89 % Allowed : 21.25 % Favored : 75.86 % 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: 0.14 (0.19), residues: 1978 helix: 1.45 (0.31), residues: 294 sheet: 0.41 (0.22), residues: 573 loop : -0.41 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 252 TYR 0.041 0.002 TYR E 214 PHE 0.037 0.002 PHE E 55 TRP 0.026 0.002 TRP A 361 HIS 0.010 0.001 HIS D 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (17259) covalent geometry : angle 0.60745 / 0.32 (23366) SS BOND : bond 0.00298 / 0.15 ( 16) SS BOND : angle 1.51516 / 0.91 ( 32) hydrogen bonds : bond 0.04085 / 2.65 ( 560) hydrogen bonds : angle 5.16177 / 3.54 ( 1413) metal coordination : bond 0.01343 / 0.81 ( 12) link_BETA1-4 : bond 0.00390 / 0.25 ( 11) link_BETA1-4 : angle 1.48941 / 0.92 ( 33) link_BETA1-6 : bond 0.00276 / 0.14 ( 4) link_BETA1-6 : angle 1.31225 / 0.77 ( 12) link_NAG-ASN : bond 0.00327 / 0.18 ( 18) link_NAG-ASN : angle 2.34261 / 1.76 ( 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 660 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 608 time to evaluate : 0.529 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 120 ILE cc_start: 0.8389 (mt) cc_final: 0.7983 (pt) REVERT: A 121 ILE cc_start: 0.8038 (tt) cc_final: 0.7437 (pt) REVERT: A 130 SER cc_start: 0.7396 (t) cc_final: 0.6515 (t) REVERT: A 150 LYS cc_start: 0.8011 (ttpp) cc_final: 0.7251 (ttpp) REVERT: A 153 ILE cc_start: 0.8248 (mt) cc_final: 0.7760 (tp) REVERT: A 154 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6756 (mt-10) REVERT: A 156 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6517 (mm-30) REVERT: A 372 ARG cc_start: 0.7167 (ttp-110) cc_final: 0.6908 (ptm-80) REVERT: A 375 VAL cc_start: 0.8223 (t) cc_final: 0.7874 (p) REVERT: A 428 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6508 (mt-10) REVERT: A 438 VAL cc_start: 0.8313 (t) cc_final: 0.7873 (p) REVERT: A 447 ASN cc_start: 0.7713 (m-40) cc_final: 0.7437 (m-40) REVERT: A 511 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 527 PHE cc_start: 0.7775 (p90) cc_final: 0.7265 (p90) REVERT: A 543 ILE cc_start: 0.8672 (mm) cc_final: 0.8355 (mt) REVERT: A 583 LYS cc_start: 0.7883 (tptt) cc_final: 0.7613 (tptt) REVERT: A 585 ASP cc_start: 0.6630 (t0) cc_final: 0.6263 (t0) REVERT: D 45 GLU cc_start: 0.7616 (tt0) cc_final: 0.7197 (tt0) REVERT: D 85 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.7082 (t0) REVERT: D 101 MET cc_start: 0.6923 (mmm) cc_final: 0.6483 (mmm) REVERT: D 105 LYS cc_start: 0.7893 (mttt) cc_final: 0.7443 (mtmt) REVERT: D 120 ILE cc_start: 0.8530 (mt) cc_final: 0.8307 (mm) REVERT: D 134 ASP cc_start: 0.6531 (p0) cc_final: 0.6286 (p0) REVERT: D 135 GLN cc_start: 0.7146 (mm110) cc_final: 0.6676 (mm110) REVERT: D 141 ILE cc_start: 0.7761 (mt) cc_final: 0.7503 (mm) REVERT: D 142 SER cc_start: 0.8060 (t) cc_final: 0.7269 (p) REVERT: D 143 ILE cc_start: 0.7854 (pt) cc_final: 0.7637 (pt) REVERT: D 156 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6390 (mm-30) REVERT: D 215 GLN cc_start: 0.7648 (mt0) cc_final: 0.7130 (mt0) REVERT: D 241 GLN cc_start: 0.7656 (pp30) cc_final: 0.7146 (pp30) REVERT: D 244 ASP cc_start: 0.7083 (t70) cc_final: 0.6406 (t70) REVERT: D 270 THR cc_start: 0.7260 (p) cc_final: 0.7046 (t) REVERT: D 287 THR cc_start: 0.7359 (t) cc_final: 0.6965 (m) REVERT: D 315 MET cc_start: 0.6268 (mmm) cc_final: 0.5915 (mmm) REVERT: D 330 LEU cc_start: 0.7607 (mt) cc_final: 0.6983 (mt) REVERT: D 342 GLN cc_start: 0.8106 (mp10) cc_final: 0.7359 (mp10) REVERT: D 345 GLN cc_start: 0.7888 (tt0) cc_final: 0.7478 (tt0) REVERT: D 362 VAL cc_start: 0.8113 (t) cc_final: 0.7833 (p) REVERT: D 373 LYS cc_start: 0.8325 (tttt) cc_final: 0.7839 (ttmm) REVERT: D 404 LEU cc_start: 0.7862 (mp) cc_final: 0.7605 (mt) REVERT: D 405 PHE cc_start: 0.7627 (m-10) cc_final: 0.7339 (m-10) REVERT: D 428 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6437 (mt-10) REVERT: D 445 LEU cc_start: 0.8403 (tp) cc_final: 0.8144 (mt) REVERT: D 453 LYS cc_start: 0.7353 (pttt) cc_final: 0.7006 (pttt) REVERT: D 465 TYR cc_start: 0.7787 (m-80) cc_final: 0.7321 (m-80) REVERT: D 512 ASP cc_start: 0.6988 (t0) cc_final: 0.6720 (t0) REVERT: D 544 TRP cc_start: 0.8126 (m100) cc_final: 0.7692 (m100) REVERT: D 573 HIS cc_start: 0.7474 (m170) cc_final: 0.7008 (m170) REVERT: D 577 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7294 (mmtt) REVERT: D 599 LEU cc_start: 0.7881 (mt) cc_final: 0.7650 (mt) REVERT: E 76 THR cc_start: 0.7711 (m) cc_final: 0.7475 (p) REVERT: E 100 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: E 126 ASP cc_start: 0.8031 (m-30) cc_final: 0.7359 (m-30) REVERT: E 131 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6470 (mt-10) REVERT: E 136 HIS cc_start: 0.7345 (m-70) cc_final: 0.6998 (m-70) REVERT: E 143 ILE cc_start: 0.8288 (mm) cc_final: 0.7848 (tp) REVERT: E 154 GLU cc_start: 0.7071 (tt0) cc_final: 0.6721 (tt0) REVERT: E 180 TRP cc_start: 0.8316 (m100) cc_final: 0.8101 (m100) REVERT: E 182 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6843 (mm-40) REVERT: E 209 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6709 (mm-30) REVERT: E 212 MET cc_start: 0.6402 (mmm) cc_final: 0.6100 (mmm) REVERT: E 224 SER cc_start: 0.7438 (m) cc_final: 0.7101 (p) REVERT: E 241 GLN cc_start: 0.8223 (pp30) cc_final: 0.7923 (pp30) REVERT: E 249 ASP cc_start: 0.6911 (m-30) cc_final: 0.6631 (m-30) REVERT: E 266 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7987 (mm) REVERT: E 299 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6156 (mt-10) REVERT: E 303 THR cc_start: 0.8376 (m) cc_final: 0.7930 (t) REVERT: E 315 MET cc_start: 0.7256 (mmm) cc_final: 0.6413 (mmm) REVERT: E 326 GLU cc_start: 0.6598 (tt0) cc_final: 0.6352 (tt0) REVERT: E 373 LYS cc_start: 0.7918 (tttt) cc_final: 0.7665 (ttpt) REVERT: E 381 GLN cc_start: 0.7634 (tp40) cc_final: 0.7086 (mm-40) REVERT: E 409 LYS cc_start: 0.8289 (mtpt) cc_final: 0.7765 (ttpt) REVERT: E 439 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7766 (mmt-90) REVERT: E 474 ASN cc_start: 0.7972 (m-40) cc_final: 0.7759 (m-40) REVERT: E 486 PHE cc_start: 0.8107 (t80) cc_final: 0.7737 (t80) REVERT: E 502 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6677 (mt-10) REVERT: E 518 ARG cc_start: 0.8191 (ttp-110) cc_final: 0.7804 (mtp-110) REVERT: E 521 MET cc_start: 0.6973 (mtp) cc_final: 0.6543 (mtp) REVERT: E 525 MET cc_start: 0.7298 (mmt) cc_final: 0.6925 (mmt) REVERT: E 527 PHE cc_start: 0.7140 (p90) cc_final: 0.6807 (p90) REVERT: E 530 SER cc_start: 0.8512 (t) cc_final: 0.8037 (p) REVERT: E 577 LYS cc_start: 0.8146 (mtpp) cc_final: 0.7801 (mtpp) REVERT: E 588 ILE cc_start: 0.8480 (mt) cc_final: 0.8076 (tt) REVERT: H 74 ARG cc_start: 0.7060 (mtt90) cc_final: 0.6706 (mtt-85) REVERT: H 76 THR cc_start: 0.7637 (m) cc_final: 0.7297 (p) REVERT: H 111 LYS cc_start: 0.7900 (pttt) cc_final: 0.7444 (pttt) REVERT: H 124 GLN cc_start: 0.7164 (tm-30) cc_final: 0.6950 (tm-30) REVERT: H 154 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6594 (mt-10) REVERT: H 156 GLU cc_start: 0.7500 (mm-30) cc_final: 0.6992 (mm-30) REVERT: H 173 ASP cc_start: 0.7317 (m-30) cc_final: 0.7082 (m-30) REVERT: H 177 ASN cc_start: 0.7957 (m110) cc_final: 0.7748 (m110) REVERT: H 200 THR cc_start: 0.5895 (OUTLIER) cc_final: 0.4236 (p) REVERT: H 212 MET cc_start: 0.6867 (mmm) cc_final: 0.6492 (mmm) REVERT: H 215 GLN cc_start: 0.7613 (mt0) cc_final: 0.7294 (mt0) REVERT: H 241 GLN cc_start: 0.8230 (pp30) cc_final: 0.7938 (pp30) REVERT: H 249 ASP cc_start: 0.6891 (m-30) cc_final: 0.6525 (m-30) REVERT: H 254 ASN cc_start: 0.7922 (m-40) cc_final: 0.7667 (m-40) REVERT: H 256 MET cc_start: 0.7500 (ttp) cc_final: 0.6988 (ttp) REVERT: H 273 LYS cc_start: 0.7608 (tttt) cc_final: 0.7248 (tptt) REVERT: H 314 PHE cc_start: 0.8509 (p90) cc_final: 0.8172 (p90) REVERT: H 315 MET cc_start: 0.7221 (mmm) cc_final: 0.6904 (mmm) REVERT: H 330 LEU cc_start: 0.8214 (tp) cc_final: 0.7863 (tt) REVERT: H 341 GLN cc_start: 0.7995 (tt0) cc_final: 0.7618 (tm-30) REVERT: H 362 VAL cc_start: 0.8419 (t) cc_final: 0.8092 (p) REVERT: H 364 ARG cc_start: 0.7893 (ptp-170) cc_final: 0.7213 (ptm160) REVERT: H 373 LYS cc_start: 0.7964 (ttpp) cc_final: 0.7346 (ttpp) REVERT: H 381 GLN cc_start: 0.7402 (tp40) cc_final: 0.7161 (mm-40) REVERT: H 394 VAL cc_start: 0.8580 (t) cc_final: 0.8202 (m) REVERT: H 397 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6283 (mm-30) REVERT: H 404 LEU cc_start: 0.8465 (mp) cc_final: 0.8160 (mt) REVERT: H 463 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7043 (mt-10) REVERT: H 471 LEU cc_start: 0.8127 (tt) cc_final: 0.7897 (tp) REVERT: H 509 THR cc_start: 0.7816 (m) cc_final: 0.7410 (p) REVERT: H 521 MET cc_start: 0.7309 (mtp) cc_final: 0.6782 (mtp) REVERT: H 575 MET cc_start: 0.6734 (tpp) cc_final: 0.6384 (tpp) REVERT: H 593 PHE cc_start: 0.8144 (t80) cc_final: 0.7649 (t80) REVERT: H 594 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6538 (mm-30) outliers start: 52 outliers final: 41 residues processed: 634 average time/residue: 0.1301 time to fit residues: 120.0267 Evaluate side-chains 650 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 604 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 220 ASN Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 269 CYS 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 493 ASN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain D residue 85 ASP 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 469 VAL 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 102 PHE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 156 GLU 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 331 GLU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 497 LEU 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 H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE 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 200 THR Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 455 GLN Chi-restraints excluded: chain H residue 496 ILE 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: 0.4980 chunk 145 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 113 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 93 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 HIS D 505 GLN E 487 HIS H 136 HIS ** H 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 ASN H 302 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123680 restraints weight = 26622.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127791 restraints weight = 14185.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.130550 restraints weight = 8983.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132330 restraints weight = 6310.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133583 restraints weight = 4825.831| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.389 17320 Z= 0.232 Angle : 0.819 59.200 23497 Z= 0.457 Chirality : 0.046 0.707 2603 Planarity : 0.004 0.048 2976 Dihedral : 4.881 46.336 2177 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.77 % Allowed : 22.09 % Favored : 75.14 % Cbeta Deviations : 0.05 % 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: 0.14 (0.19), residues: 1978 helix: 1.47 (0.31), residues: 294 sheet: 0.40 (0.22), residues: 575 loop : -0.41 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 74 TYR 0.038 0.002 TYR E 214 PHE 0.036 0.002 PHE E 55 TRP 0.025 0.002 TRP A 361 HIS 0.009 0.001 HIS D 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.23 (17259) covalent geometry : angle 0.80854 / 0.46 (23366) SS BOND : bond 0.00255 / 0.14 ( 16) SS BOND : angle 1.63559 / 1.01 ( 32) hydrogen bonds : bond 0.03997 / 2.59 ( 560) hydrogen bonds : angle 5.16122 / 3.54 ( 1413) metal coordination : bond 0.00993 / 0.57 ( 12) link_BETA1-4 : bond 0.00359 / 0.23 ( 11) link_BETA1-4 : angle 1.47046 / 0.90 ( 33) link_BETA1-6 : bond 0.00312 / 0.16 ( 4) link_BETA1-6 : angle 1.34499 / 0.79 ( 12) link_NAG-ASN : bond 0.00280 / 0.16 ( 18) link_NAG-ASN : angle 2.33942 / 1.76 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2876.40 seconds wall clock time: 50 minutes 19.99 seconds (3019.99 seconds total)