Starting phenix.real_space_refine on Sat Aug 23 17:43:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvi_52435/08_2025/9hvi_52435.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvi_52435/08_2025/9hvi_52435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hvi_52435/08_2025/9hvi_52435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvi_52435/08_2025/9hvi_52435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hvi_52435/08_2025/9hvi_52435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvi_52435/08_2025/9hvi_52435.map" } resolution = 2.46 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= -0.001 sd= 0.024 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 4 6.06 5 S 44 5.16 5 Cl 1 4.86 5 C 8502 2.51 5 N 2206 2.21 5 O 2593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13352 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5537 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 650} Chain: "E" Number of atoms: 5550 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 695, 5537 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 650} Conformer: "B" Number of residues, atoms: 695, 5537 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 650} bond proxies already assigned to first conformer: 5679 Chain: "H" Number of atoms: 945 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Conformer: "C" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} bond proxies already assigned to first conformer: 957 Chain: "Q" Number of atoms: 945 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Conformer: "B" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} bond proxies already assigned to first conformer: 957 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Unusual residues: {' CA': 1, ' ZN': 2, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 60 Unusual residues: {' CA': 1, ' CL': 1, ' ZN': 2, 'NAG': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER E 155 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER E 155 " occ=0.50 residue: pdb=" N AVAL E 660 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL E 660 " occ=0.50 Time building chain proxies: 4.82, per 1000 atoms: 0.36 Number of scatterers: 13352 At special positions: 0 Unit cell: (99.68, 145.07, 99.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 2 19.99 Cl 1 17.00 S 44 16.00 O 2593 8.00 N 2206 7.00 C 8502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A 801 " - " ASN A 121 " " NAG A 802 " - " ASN A 140 " " NAG A 804 " - " ASN A 459 " " NAG E 801 " - " ASN E 121 " " NAG E 802 " - " ASN E 140 " " NAG E 804 " - " ASN E 459 " Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 879.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" NE2 HIS A 553 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" NE2 HIS A 377 " pdb=" ZN E 805 " pdb="ZN ZN E 805 " - pdb=" NE2 HIS E 553 " pdb=" ZN E 806 " pdb="ZN ZN E 806 " - pdb=" NE2 HIS E 377 " 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 13 sheets defined 39.1% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.573A pdb=" N LEU A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 78 Processing helix chain 'A' and resid 86 through 104 Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 298 through 308 removed outlier: 3.972A pdb=" N LYS A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 removed outlier: 3.615A pdb=" N SER A 338 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 409 removed outlier: 3.709A pdb=" N VAL A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 427 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 438 through 445 removed outlier: 4.392A pdb=" N GLU A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.637A pdb=" N SER A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.374A pdb=" N PHE A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 527 " --> pdb=" O VAL A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 566 removed outlier: 3.698A pdb=" N VAL A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 590 Processing helix chain 'A' and resid 597 through 617 Processing helix chain 'A' and resid 618 through 626 Processing helix chain 'A' and resid 629 through 652 Processing helix chain 'A' and resid 657 through 675 removed outlier: 4.294A pdb=" N GLU A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG A 673 " --> pdb=" O MET A 669 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 713 Processing helix chain 'A' and resid 714 through 718 Processing helix chain 'A' and resid 720 through 746 removed outlier: 3.964A pdb=" N LEU A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 65 removed outlier: 3.548A pdb=" N LEU E 65 " --> pdb=" O PHE E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.516A pdb=" N ILE E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 104 Processing helix chain 'E' and resid 181 through 191 Processing helix chain 'E' and resid 209 through 221 Processing helix chain 'E' and resid 230 through 235 Processing helix chain 'E' and resid 241 through 245 Processing helix chain 'E' and resid 282 through 286 Processing helix chain 'E' and resid 298 through 308 removed outlier: 4.297A pdb=" N LYS E 304 " --> pdb=" O TYR E 300 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 407 Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 428 through 438 Processing helix chain 'E' and resid 438 through 445 removed outlier: 4.424A pdb=" N GLU E 444 " --> pdb=" O ARG E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 481 Processing helix chain 'E' and resid 492 through 501 removed outlier: 3.668A pdb=" N SER E 496 " --> pdb=" O SER E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 527 removed outlier: 4.360A pdb=" N PHE E 524 " --> pdb=" O ASP E 520 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 527 " --> pdb=" O VAL E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 566 removed outlier: 3.710A pdb=" N VAL E 562 " --> pdb=" O THR E 558 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR E 566 " --> pdb=" O VAL E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 590 Processing helix chain 'E' and resid 597 through 617 Processing helix chain 'E' and resid 618 through 626 Processing helix chain 'E' and resid 629 through 652 Processing helix chain 'E' and resid 657 through 675 removed outlier: 4.303A pdb=" N GLU E 672 " --> pdb=" O LEU E 668 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG E 673 " --> pdb=" O MET E 669 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE E 675 " --> pdb=" O LEU E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 713 Processing helix chain 'E' and resid 714 through 718 removed outlier: 3.580A pdb=" N LYS E 718 " --> pdb=" O ILE E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 720 through 745 Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'Q' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 119 removed outlier: 5.572A pdb=" N GLY A 446 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A 371 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 448 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A 531 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 461 " --> pdb=" O THR A 538 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 139 through 140 removed outlier: 3.808A pdb=" N PHE A 139 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 163 removed outlier: 7.408A pdb=" N GLY A 256 " --> pdb=" O ALA A 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 174 through 176 removed outlier: 6.008A pdb=" N VAL A 175 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ARG A 204 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 225 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE A 297 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 227 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 107 through 119 removed outlier: 3.597A pdb=" N SER E 107 " --> pdb=" O THR E 361 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N GLY E 446 " --> pdb=" O GLU E 367 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N ASP E 369 " --> pdb=" O GLY E 446 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ALA E 448 " --> pdb=" O ASP E 369 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N TYR E 371 " --> pdb=" O ALA E 448 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE E 450 " --> pdb=" O TYR E 371 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE E 373 " --> pdb=" O ILE E 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA E 531 " --> pdb=" O VAL E 447 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR E 461 " --> pdb=" O THR E 538 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 171 through 172 removed outlier: 3.641A pdb=" N PHE E 139 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY Q 57 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ARG Q 38 " --> pdb=" O ALA Q 47 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLY Q 10 " --> pdb=" O THR Q 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 171 through 172 removed outlier: 3.641A pdb=" N PHE E 139 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY Q 57 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ARG Q 38 " --> pdb=" O ALA Q 47 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR Q 113 " --> pdb=" O ALA Q 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 162 through 163 removed outlier: 7.391A pdb=" N GLY E 256 " --> pdb=" O ALA E 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 174 through 176 removed outlier: 6.076A pdb=" N VAL E 175 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ARG E 204 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL E 225 " --> pdb=" O HIS E 295 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE E 297 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU E 227 " --> pdb=" O ILE E 297 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.235A pdb=" N ALA H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG H 38 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.235A pdb=" N ALA H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG H 38 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 6 through 7 593 hydrogen bonds defined for protein. 1648 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: 2.55 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4249 1.34 - 1.46: 3309 1.46 - 1.58: 6065 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 13701 Sorted by residual: bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.571 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C1 MAN I 4 " pdb=" C2 MAN I 4 " ideal model delta sigma weight residual 1.526 1.568 -0.042 2.00e-02 2.50e+03 4.31e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 4.10e+00 bond pdb=" C1 MAN I 4 " pdb=" O5 MAN I 4 " ideal model delta sigma weight residual 1.399 1.436 -0.037 2.00e-02 2.50e+03 3.49e+00 bond pdb=" C1 MAN F 5 " pdb=" C2 MAN F 5 " ideal model delta sigma weight residual 1.526 1.561 -0.035 2.00e-02 2.50e+03 3.08e+00 ... (remaining 13696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 18319 2.63 - 5.27: 230 5.27 - 7.90: 23 7.90 - 10.54: 7 10.54 - 13.17: 1 Bond angle restraints: 18580 Sorted by residual: angle pdb=" CA LEU A 188 " pdb=" CB LEU A 188 " pdb=" CG LEU A 188 " ideal model delta sigma weight residual 116.30 129.47 -13.17 3.50e+00 8.16e-02 1.42e+01 angle pdb=" N VAL A 329 " pdb=" CA VAL A 329 " pdb=" C VAL A 329 " ideal model delta sigma weight residual 113.53 109.91 3.62 9.80e-01 1.04e+00 1.37e+01 angle pdb=" N VAL E 329 " pdb=" CA VAL E 329 " pdb=" C VAL E 329 " ideal model delta sigma weight residual 113.42 109.30 4.12 1.17e+00 7.31e-01 1.24e+01 angle pdb=" CA GLU E 648 " pdb=" CB GLU E 648 " pdb=" CG GLU E 648 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CB GLU E 648 " pdb=" CG GLU E 648 " pdb=" CD GLU E 648 " ideal model delta sigma weight residual 112.60 118.01 -5.41 1.70e+00 3.46e-01 1.01e+01 ... (remaining 18575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 7779 21.86 - 43.72: 535 43.72 - 65.58: 100 65.58 - 87.45: 34 87.45 - 109.31: 20 Dihedral angle restraints: 8468 sinusoidal: 3728 harmonic: 4740 Sorted by residual: dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.40 109.31 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C3 MAN I 4 " pdb=" C1 MAN I 4 " pdb=" C2 MAN I 4 " pdb=" O5 MAN I 4 " ideal model delta sinusoidal sigma weight residual -53.57 54.57 -108.14 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.36 108.07 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 8465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1776 0.073 - 0.146: 226 0.146 - 0.219: 3 0.219 - 0.292: 3 0.292 - 0.365: 1 Chirality restraints: 2009 Sorted by residual: chirality pdb=" CB ILE A 194 " pdb=" CA ILE A 194 " pdb=" CG1 ILE A 194 " pdb=" CG2 ILE A 194 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2006 not shown) Planarity restraints: 2396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " -0.015 2.00e-02 2.50e+03 1.41e-02 4.96e+00 pdb=" CG TRP H 36 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 102 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" CD GLU A 102 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU A 102 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 102 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 387 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A 388 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " 0.023 5.00e-02 4.00e+02 ... (remaining 2393 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 186 2.59 - 3.17: 11371 3.17 - 3.75: 22177 3.75 - 4.32: 31346 4.32 - 4.90: 50429 Nonbonded interactions: 115509 Sorted by model distance: nonbonded pdb=" OD1 ASP E 387 " pdb="ZN ZN E 806 " model vdw 2.013 2.230 nonbonded pdb=" OD1 ASP A 387 " pdb="ZN ZN A 806 " model vdw 2.017 2.230 nonbonded pdb=" O PRO A 273 " pdb=" OH TYR E 733 " model vdw 2.107 3.040 nonbonded pdb=" NE2 GLN H 119 " pdb=" OG1 THR H 121 " model vdw 2.111 3.120 nonbonded pdb=" OH TYR A 733 " pdb=" O PRO E 273 " model vdw 2.133 3.040 ... (remaining 115504 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 56 through 154 or resid 156 through 659 or resid 661 throu \ gh 807)) selection = (chain 'E' and (resid 56 through 154 or resid 156 through 659 or resid 661 throu \ gh 807)) } ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'I' } ncs_group { reference = (chain 'H' and (resid 1 through 10 or resid 12 through 106 or resid 108 through \ 123)) selection = (chain 'Q' and (resid 1 through 10 or resid 12 through 106 or resid 108 through \ 123)) } 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=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.930 Find NCS groups from input model: 0.280 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.004 0.052 13725 Z= 0.186 Angle : 0.702 13.172 18640 Z= 0.349 Chirality : 0.046 0.365 2009 Planarity : 0.004 0.055 2390 Dihedral : 16.401 109.308 5460 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.01 % Allowed : 19.67 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 aren not related in a simple way. whole: 0.11 (0.21), residues: 1636 helix: 1.38 (0.22), residues: 513 sheet: -0.97 (0.28), residues: 302 loop : -0.26 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 320 TYR 0.020 0.001 TYR E 300 PHE 0.017 0.001 PHE A 546 TRP 0.036 0.002 TRP H 36 HIS 0.004 0.001 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00396 (13701) covalent geometry : angle 0.69539 (18580) hydrogen bonds : bond 0.13920 ( 559) hydrogen bonds : angle 5.82621 ( 1648) metal coordination : bond 0.00146 ( 4) link_ALPHA1-3 : bond 0.00805 ( 2) link_ALPHA1-3 : angle 1.48034 ( 6) link_ALPHA1-6 : bond 0.00522 ( 2) link_ALPHA1-6 : angle 1.65589 ( 6) link_BETA1-4 : bond 0.00688 ( 10) link_BETA1-4 : angle 2.01449 ( 30) link_NAG-ASN : bond 0.00337 ( 6) link_NAG-ASN : angle 1.64690 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 272 time to evaluate : 0.519 Fit side-chains REVERT: A 63 ASP cc_start: 0.8102 (t70) cc_final: 0.7456 (m-30) REVERT: A 72 LYS cc_start: 0.7590 (mmtp) cc_final: 0.7314 (ttpp) REVERT: A 623 LYS cc_start: 0.8996 (ttpp) cc_final: 0.8522 (pttm) REVERT: A 733 TYR cc_start: 0.7986 (t80) cc_final: 0.7335 (t80) REVERT: E 64 GLU cc_start: 0.7999 (tp30) cc_final: 0.7765 (tp30) REVERT: E 66 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7112 (mptp) REVERT: E 82 HIS cc_start: 0.7385 (m-70) cc_final: 0.7177 (m90) REVERT: E 473 LEU cc_start: 0.7972 (tp) cc_final: 0.7387 (tt) REVERT: E 495 GLU cc_start: 0.8865 (pt0) cc_final: 0.8472 (pp20) REVERT: E 623 LYS cc_start: 0.9006 (ttpp) cc_final: 0.8475 (pttm) REVERT: E 700 TYR cc_start: 0.7551 (m-80) cc_final: 0.7217 (m-80) REVERT: E 733 TYR cc_start: 0.7993 (t80) cc_final: 0.7317 (t80) REVERT: H 104 LEU cc_start: 0.8545 (mp) cc_final: 0.8322 (mt) REVERT: Q 22 CYS cc_start: 0.8731 (p) cc_final: 0.8508 (m) REVERT: Q 64 LYS cc_start: 0.8192 (mtpm) cc_final: 0.7946 (ptmm) REVERT: Q 80 TYR cc_start: 0.7664 (m-80) cc_final: 0.7397 (m-80) outliers start: 14 outliers final: 8 residues processed: 281 average time/residue: 0.4813 time to fit residues: 149.7807 Evaluate side-chains 179 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 171 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 624 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 328 ASN E 136 ASN E 254 GLN E 303 GLN E 328 ASN H 77 ASN H 82 GLN Q 5 GLN Q 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.107153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.074762 restraints weight = 55382.386| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.82 r_work: 0.2854 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 13725 Z= 0.236 Angle : 0.777 11.103 18640 Z= 0.387 Chirality : 0.049 0.189 2009 Planarity : 0.005 0.055 2390 Dihedral : 10.829 91.272 2392 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.60 % Allowed : 18.30 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 aren not related in a simple way. whole: -0.11 (0.20), residues: 1636 helix: 1.21 (0.22), residues: 521 sheet: -0.90 (0.28), residues: 300 loop : -0.51 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 400 TYR 0.032 0.003 TYR H 95 PHE 0.017 0.002 PHE E 546 TRP 0.015 0.002 TRP H 36 HIS 0.010 0.002 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00528 (13701) covalent geometry : angle 0.76393 (18580) hydrogen bonds : bond 0.04803 ( 559) hydrogen bonds : angle 4.85499 ( 1648) metal coordination : bond 0.06163 ( 4) link_ALPHA1-3 : bond 0.01603 ( 2) link_ALPHA1-3 : angle 2.27203 ( 6) link_ALPHA1-6 : bond 0.01010 ( 2) link_ALPHA1-6 : angle 2.76257 ( 6) link_BETA1-4 : bond 0.00936 ( 10) link_BETA1-4 : angle 2.81113 ( 30) link_NAG-ASN : bond 0.00218 ( 6) link_NAG-ASN : angle 2.14697 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8726 (t70) cc_final: 0.8113 (m-30) REVERT: A 64 GLU cc_start: 0.8765 (tp30) cc_final: 0.8405 (tp30) REVERT: A 102 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8194 (tm-30) REVERT: A 285 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: A 495 GLU cc_start: 0.8866 (pp20) cc_final: 0.8652 (pp20) REVERT: A 563 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8484 (tm-30) REVERT: A 623 LYS cc_start: 0.9168 (ttpp) cc_final: 0.8748 (pttm) REVERT: A 653 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.6834 (p90) REVERT: E 63 ASP cc_start: 0.8719 (t70) cc_final: 0.7984 (m-30) REVERT: E 64 GLU cc_start: 0.8532 (tp30) cc_final: 0.8070 (tp30) REVERT: E 66 LYS cc_start: 0.8487 (mtmm) cc_final: 0.7694 (mptp) REVERT: E 68 GLU cc_start: 0.8162 (tp30) cc_final: 0.7781 (OUTLIER) REVERT: E 72 LYS cc_start: 0.8459 (mmpt) cc_final: 0.8244 (mmtm) REVERT: E 102 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8276 (tm-30) REVERT: E 188 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8519 (mp) REVERT: E 495 GLU cc_start: 0.9001 (pt0) cc_final: 0.8672 (pp20) REVERT: E 563 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8508 (tm-30) REVERT: E 623 LYS cc_start: 0.9167 (ttpp) cc_final: 0.8707 (pttm) REVERT: E 651 GLN cc_start: 0.8605 (mp10) cc_final: 0.8103 (mm110) REVERT: H 82 GLN cc_start: 0.7946 (tp40) cc_final: 0.7534 (tp-100) REVERT: H 95 TYR cc_start: 0.8150 (m-10) cc_final: 0.7739 (m-10) REVERT: H 99 ARG cc_start: 0.8501 (ptm-80) cc_final: 0.8245 (ptm-80) REVERT: Q 82 GLN cc_start: 0.8135 (tp40) cc_final: 0.7780 (tp-100) REVERT: Q 95 TYR cc_start: 0.8202 (m-10) cc_final: 0.7924 (m-10) REVERT: Q 100 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8430 (mmm160) outliers start: 50 outliers final: 16 residues processed: 214 average time/residue: 0.5469 time to fit residues: 127.8282 Evaluate side-chains 165 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 100 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 95 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 139 optimal weight: 0.0970 chunk 43 optimal weight: 7.9990 chunk 154 optimal weight: 40.0000 chunk 136 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 254 GLN E 328 ASN E 340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.106700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.074004 restraints weight = 59571.350| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.88 r_work: 0.2840 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13725 Z= 0.133 Angle : 0.623 10.556 18640 Z= 0.306 Chirality : 0.043 0.158 2009 Planarity : 0.004 0.044 2390 Dihedral : 9.570 88.648 2384 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.17 % Allowed : 19.24 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 aren not related in a simple way. whole: 0.25 (0.21), residues: 1636 helix: 1.76 (0.22), residues: 523 sheet: -0.81 (0.28), residues: 286 loop : -0.46 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 320 TYR 0.023 0.001 TYR A 700 PHE 0.017 0.001 PHE E 506 TRP 0.012 0.001 TRP H 36 HIS 0.005 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00301 (13701) covalent geometry : angle 0.61273 (18580) hydrogen bonds : bond 0.03904 ( 559) hydrogen bonds : angle 4.52412 ( 1648) metal coordination : bond 0.00338 ( 4) link_ALPHA1-3 : bond 0.01703 ( 2) link_ALPHA1-3 : angle 1.81872 ( 6) link_ALPHA1-6 : bond 0.01022 ( 2) link_ALPHA1-6 : angle 2.05124 ( 6) link_BETA1-4 : bond 0.00794 ( 10) link_BETA1-4 : angle 2.32385 ( 30) link_NAG-ASN : bond 0.00394 ( 6) link_NAG-ASN : angle 1.70945 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8742 (t70) cc_final: 0.8127 (m-30) REVERT: A 64 GLU cc_start: 0.8665 (tp30) cc_final: 0.8275 (tp30) REVERT: A 68 GLU cc_start: 0.8089 (tp30) cc_final: 0.7754 (mp0) REVERT: A 102 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8304 (tm-30) REVERT: A 181 ARG cc_start: 0.8685 (mtm180) cc_final: 0.8265 (mtm180) REVERT: A 285 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: A 495 GLU cc_start: 0.8814 (pp20) cc_final: 0.8603 (pp20) REVERT: A 537 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7921 (t80) REVERT: A 563 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8599 (tm-30) REVERT: A 616 MET cc_start: 0.9076 (tpp) cc_final: 0.8744 (tpp) REVERT: A 623 LYS cc_start: 0.9161 (ttpp) cc_final: 0.8784 (pttm) REVERT: A 653 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6711 (p90) REVERT: A 700 TYR cc_start: 0.7797 (m-80) cc_final: 0.7433 (m-80) REVERT: E 63 ASP cc_start: 0.8735 (t70) cc_final: 0.8075 (m-30) REVERT: E 64 GLU cc_start: 0.8530 (tp30) cc_final: 0.7988 (tp30) REVERT: E 66 LYS cc_start: 0.8538 (mtmm) cc_final: 0.7777 (mptp) REVERT: E 68 GLU cc_start: 0.8128 (tp30) cc_final: 0.7766 (mp0) REVERT: E 102 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8348 (tm-30) REVERT: E 495 GLU cc_start: 0.9002 (pt0) cc_final: 0.8552 (pp20) REVERT: E 537 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7604 (t80) REVERT: E 563 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8594 (tm-30) REVERT: E 623 LYS cc_start: 0.9153 (ttpp) cc_final: 0.8728 (pttp) REVERT: E 653 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6693 (p90) REVERT: E 663 MET cc_start: 0.7756 (mtp) cc_final: 0.7327 (mtm) REVERT: H 3 GLN cc_start: 0.7807 (tp40) cc_final: 0.7532 (tp40) REVERT: H 82 GLN cc_start: 0.7940 (tp40) cc_final: 0.7572 (tp-100) REVERT: H 95 TYR cc_start: 0.8454 (m-80) cc_final: 0.7892 (m-10) REVERT: Q 64 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8405 (ptmt) REVERT: Q 82 GLN cc_start: 0.8090 (tp40) cc_final: 0.7693 (tp-100) REVERT: Q 95 TYR cc_start: 0.8195 (m-80) cc_final: 0.7892 (m-10) outliers start: 44 outliers final: 15 residues processed: 187 average time/residue: 0.5513 time to fit residues: 113.1970 Evaluate side-chains 161 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 396 HIS Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain E residue 651 GLN Chi-restraints excluded: chain E residue 653 PHE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain Q residue 64 LYS Chi-restraints excluded: chain Q residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 328 ASN E 340 GLN H 77 ASN ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.102218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.069114 restraints weight = 61184.782| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.92 r_work: 0.2730 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 13725 Z= 0.288 Angle : 0.730 12.929 18640 Z= 0.363 Chirality : 0.048 0.182 2009 Planarity : 0.005 0.049 2390 Dihedral : 9.206 87.580 2384 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.10 % Allowed : 18.88 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 aren not related in a simple way. whole: -0.08 (0.21), residues: 1636 helix: 1.44 (0.22), residues: 521 sheet: -0.98 (0.28), residues: 284 loop : -0.63 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 320 TYR 0.051 0.002 TYR E 300 PHE 0.015 0.002 PHE E 737 TRP 0.011 0.002 TRP E 381 HIS 0.006 0.002 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00674 (13701) covalent geometry : angle 0.71978 (18580) hydrogen bonds : bond 0.04850 ( 559) hydrogen bonds : angle 4.77981 ( 1648) metal coordination : bond 0.00350 ( 4) link_ALPHA1-3 : bond 0.01517 ( 2) link_ALPHA1-3 : angle 1.85497 ( 6) link_ALPHA1-6 : bond 0.00727 ( 2) link_ALPHA1-6 : angle 1.89022 ( 6) link_BETA1-4 : bond 0.00717 ( 10) link_BETA1-4 : angle 2.54062 ( 30) link_NAG-ASN : bond 0.00210 ( 6) link_NAG-ASN : angle 1.91164 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8044 (tp30) cc_final: 0.7714 (mp0) REVERT: A 169 MET cc_start: 0.6982 (mmt) cc_final: 0.6196 (mmt) REVERT: A 495 GLU cc_start: 0.8792 (pp20) cc_final: 0.8537 (pp20) REVERT: A 511 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8299 (ttt90) REVERT: A 537 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8277 (t80) REVERT: A 616 MET cc_start: 0.9248 (tpp) cc_final: 0.8839 (tpp) REVERT: A 651 GLN cc_start: 0.8447 (mm110) cc_final: 0.7753 (mp10) REVERT: E 68 GLU cc_start: 0.8037 (tp30) cc_final: 0.7758 (mp0) REVERT: E 102 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8374 (tm-30) REVERT: E 300 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7596 (t80) REVERT: E 309 MET cc_start: 0.9012 (tpt) cc_final: 0.8783 (tpt) REVERT: E 511 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8205 (ttt90) REVERT: E 537 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.8296 (t80) REVERT: E 616 MET cc_start: 0.9272 (tpp) cc_final: 0.9029 (tpp) REVERT: E 651 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7954 (mp10) REVERT: E 653 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7462 (p90) REVERT: E 664 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8498 (mmm) REVERT: E 749 VAL cc_start: 0.8463 (m) cc_final: 0.8236 (m) REVERT: H 82 GLN cc_start: 0.8033 (tp40) cc_final: 0.7726 (tp40) REVERT: H 95 TYR cc_start: 0.8524 (m-80) cc_final: 0.7874 (m-10) REVERT: Q 95 TYR cc_start: 0.8286 (m-80) cc_final: 0.7894 (m-10) outliers start: 43 outliers final: 14 residues processed: 167 average time/residue: 0.5903 time to fit residues: 107.6514 Evaluate side-chains 151 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain E residue 511 ARG Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain E residue 651 GLN Chi-restraints excluded: chain E residue 653 PHE Chi-restraints excluded: chain E residue 664 MET Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 64 LYS Chi-restraints excluded: chain Q residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 21 optimal weight: 0.0980 chunk 92 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN E 651 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.071335 restraints weight = 76569.895| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 4.31 r_work: 0.2769 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13725 Z= 0.126 Angle : 0.613 11.751 18640 Z= 0.301 Chirality : 0.043 0.183 2009 Planarity : 0.004 0.043 2390 Dihedral : 8.464 83.389 2384 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.23 % Allowed : 19.52 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 aren not related in a simple way. whole: 0.23 (0.21), residues: 1636 helix: 1.79 (0.22), residues: 523 sheet: -0.88 (0.28), residues: 286 loop : -0.48 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 320 TYR 0.034 0.001 TYR E 300 PHE 0.012 0.001 PHE E 737 TRP 0.016 0.001 TRP H 36 HIS 0.004 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00286 (13701) covalent geometry : angle 0.60257 (18580) hydrogen bonds : bond 0.03762 ( 559) hydrogen bonds : angle 4.48549 ( 1648) metal coordination : bond 0.00136 ( 4) link_ALPHA1-3 : bond 0.01821 ( 2) link_ALPHA1-3 : angle 1.97679 ( 6) link_ALPHA1-6 : bond 0.00742 ( 2) link_ALPHA1-6 : angle 1.63402 ( 6) link_BETA1-4 : bond 0.00651 ( 10) link_BETA1-4 : angle 2.33830 ( 30) link_NAG-ASN : bond 0.00406 ( 6) link_NAG-ASN : angle 1.61805 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.524 Fit side-chains REVERT: A 68 GLU cc_start: 0.7963 (tp30) cc_final: 0.7699 (mp0) REVERT: A 285 GLU cc_start: 0.8509 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 334 THR cc_start: 0.9053 (m) cc_final: 0.8712 (p) REVERT: A 495 GLU cc_start: 0.8812 (pp20) cc_final: 0.8575 (pp20) REVERT: A 537 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.8170 (t80) REVERT: A 563 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8632 (tm-30) REVERT: A 616 MET cc_start: 0.9161 (tpp) cc_final: 0.8792 (tpp) REVERT: A 623 LYS cc_start: 0.9208 (ttpp) cc_final: 0.8644 (pttm) REVERT: A 648 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8024 (tm-30) REVERT: A 651 GLN cc_start: 0.8438 (mm110) cc_final: 0.7808 (mp10) REVERT: A 653 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7449 (p90) REVERT: A 663 MET cc_start: 0.7831 (mtp) cc_final: 0.7516 (mtm) REVERT: E 68 GLU cc_start: 0.8008 (tp30) cc_final: 0.7794 (mp0) REVERT: E 102 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8439 (tm-30) REVERT: E 285 GLU cc_start: 0.8594 (tm-30) cc_final: 0.7846 (tm-30) REVERT: E 324 LYS cc_start: 0.9039 (ttmm) cc_final: 0.8804 (tmmt) REVERT: E 537 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.8095 (t80) REVERT: E 616 MET cc_start: 0.9250 (tpp) cc_final: 0.9049 (tpp) REVERT: E 651 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: E 749 VAL cc_start: 0.8270 (m) cc_final: 0.8011 (m) REVERT: H 95 TYR cc_start: 0.8518 (m-80) cc_final: 0.7793 (m-10) REVERT: Q 95 TYR cc_start: 0.8291 (m-80) cc_final: 0.7910 (m-10) REVERT: Q 100 ARG cc_start: 0.8678 (mmm160) cc_final: 0.8390 (mmm160) outliers start: 31 outliers final: 11 residues processed: 159 average time/residue: 0.5661 time to fit residues: 98.6324 Evaluate side-chains 148 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain E residue 651 GLN Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 0.0470 chunk 71 optimal weight: 0.3980 chunk 121 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 651 GLN H 77 ASN H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.104599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.071294 restraints weight = 79490.165| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 4.35 r_work: 0.2769 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13725 Z= 0.129 Angle : 0.611 11.308 18640 Z= 0.299 Chirality : 0.043 0.175 2009 Planarity : 0.004 0.045 2390 Dihedral : 8.115 83.427 2384 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.95 % Allowed : 20.46 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 aren not related in a simple way. whole: 0.34 (0.21), residues: 1636 helix: 1.90 (0.22), residues: 523 sheet: -0.80 (0.28), residues: 286 loop : -0.44 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 320 TYR 0.023 0.001 TYR E 300 PHE 0.011 0.001 PHE A 506 TRP 0.019 0.001 TRP H 36 HIS 0.004 0.001 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00298 (13701) covalent geometry : angle 0.60063 (18580) hydrogen bonds : bond 0.03647 ( 559) hydrogen bonds : angle 4.41772 ( 1648) metal coordination : bond 0.00083 ( 4) link_ALPHA1-3 : bond 0.01804 ( 2) link_ALPHA1-3 : angle 2.07109 ( 6) link_ALPHA1-6 : bond 0.00653 ( 2) link_ALPHA1-6 : angle 1.63133 ( 6) link_BETA1-4 : bond 0.00674 ( 10) link_BETA1-4 : angle 2.33946 ( 30) link_NAG-ASN : bond 0.00361 ( 6) link_NAG-ASN : angle 1.55883 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.532 Fit side-chains REVERT: A 68 GLU cc_start: 0.7964 (tp30) cc_final: 0.7702 (mp0) REVERT: A 276 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7893 (mm-30) REVERT: A 285 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: A 334 THR cc_start: 0.9076 (m) cc_final: 0.8730 (p) REVERT: A 489 GLU cc_start: 0.8505 (pm20) cc_final: 0.8296 (mp0) REVERT: A 495 GLU cc_start: 0.8804 (pp20) cc_final: 0.8557 (pp20) REVERT: A 537 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8106 (t80) REVERT: A 616 MET cc_start: 0.9169 (tpp) cc_final: 0.8928 (tpp) REVERT: A 623 LYS cc_start: 0.9209 (ttpp) cc_final: 0.8676 (pttm) REVERT: A 648 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8080 (tm-30) REVERT: A 651 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7886 (mp10) REVERT: A 653 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7348 (p90) REVERT: A 663 MET cc_start: 0.7806 (mtp) cc_final: 0.7445 (mtm) REVERT: E 68 GLU cc_start: 0.8017 (tp30) cc_final: 0.7803 (mp0) REVERT: E 110 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8887 (mp) REVERT: E 285 GLU cc_start: 0.8635 (tm-30) cc_final: 0.7913 (tm-30) REVERT: E 324 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8806 (tmmt) REVERT: E 537 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.8094 (t80) REVERT: H 82 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7875 (tp40) REVERT: H 95 TYR cc_start: 0.8538 (m-80) cc_final: 0.7738 (m-10) REVERT: Q 64 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8217 (ptmt) REVERT: Q 95 TYR cc_start: 0.8327 (m-80) cc_final: 0.7787 (m-10) outliers start: 27 outliers final: 12 residues processed: 151 average time/residue: 0.5551 time to fit residues: 92.0301 Evaluate side-chains 150 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain Q residue 64 LYS Chi-restraints excluded: chain Q residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 93 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 159 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN H 77 ASN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.105629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.072402 restraints weight = 75550.686| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.29 r_work: 0.2787 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13725 Z= 0.117 Angle : 0.609 12.397 18640 Z= 0.296 Chirality : 0.042 0.169 2009 Planarity : 0.004 0.043 2390 Dihedral : 7.823 82.214 2384 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.23 % Allowed : 20.53 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 aren not related in a simple way. whole: 0.39 (0.21), residues: 1636 helix: 1.99 (0.22), residues: 523 sheet: -0.79 (0.28), residues: 286 loop : -0.44 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 320 TYR 0.020 0.001 TYR E 300 PHE 0.014 0.001 PHE E 506 TRP 0.018 0.001 TRP H 36 HIS 0.004 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00268 (13701) covalent geometry : angle 0.59900 (18580) hydrogen bonds : bond 0.03502 ( 559) hydrogen bonds : angle 4.35863 ( 1648) metal coordination : bond 0.00063 ( 4) link_ALPHA1-3 : bond 0.01896 ( 2) link_ALPHA1-3 : angle 2.11327 ( 6) link_ALPHA1-6 : bond 0.00624 ( 2) link_ALPHA1-6 : angle 1.62570 ( 6) link_BETA1-4 : bond 0.00680 ( 10) link_BETA1-4 : angle 2.30932 ( 30) link_NAG-ASN : bond 0.00386 ( 6) link_NAG-ASN : angle 1.51344 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.494 Fit side-chains REVERT: A 68 GLU cc_start: 0.7965 (tp30) cc_final: 0.7711 (mp0) REVERT: A 276 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7888 (mm-30) REVERT: A 285 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: A 334 THR cc_start: 0.9088 (m) cc_final: 0.8765 (p) REVERT: A 495 GLU cc_start: 0.8786 (pp20) cc_final: 0.8555 (pp20) REVERT: A 537 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.8088 (t80) REVERT: A 563 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8643 (tm-30) REVERT: A 616 MET cc_start: 0.9155 (tpp) cc_final: 0.8921 (tpp) REVERT: A 623 LYS cc_start: 0.9220 (ttpp) cc_final: 0.8693 (pttm) REVERT: A 648 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8092 (tm-30) REVERT: A 651 GLN cc_start: 0.8468 (mm-40) cc_final: 0.7821 (mp10) REVERT: A 653 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.7076 (p90) REVERT: A 663 MET cc_start: 0.7796 (mtp) cc_final: 0.7415 (mtm) REVERT: A 664 MET cc_start: 0.8528 (mmm) cc_final: 0.8218 (mtm) REVERT: E 109 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8543 (mm-30) REVERT: E 285 GLU cc_start: 0.8661 (tm-30) cc_final: 0.7943 (tm-30) REVERT: E 324 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8797 (tmmt) REVERT: E 537 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.8084 (t80) REVERT: E 651 GLN cc_start: 0.8453 (mp10) cc_final: 0.8013 (mp10) REVERT: H 82 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7932 (tp40) REVERT: H 95 TYR cc_start: 0.8539 (m-80) cc_final: 0.7742 (m-10) REVERT: Q 64 LYS cc_start: 0.8618 (ptmm) cc_final: 0.8266 (ptmt) REVERT: Q 95 TYR cc_start: 0.8361 (m-80) cc_final: 0.7814 (m-10) outliers start: 31 outliers final: 12 residues processed: 156 average time/residue: 0.5534 time to fit residues: 95.2820 Evaluate side-chains 149 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 144 optimal weight: 0.0980 chunk 115 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN H 77 ASN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.071500 restraints weight = 70607.523| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 4.20 r_work: 0.2773 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13725 Z= 0.146 Angle : 0.636 11.707 18640 Z= 0.308 Chirality : 0.043 0.168 2009 Planarity : 0.004 0.044 2390 Dihedral : 7.703 82.305 2384 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.38 % Allowed : 20.32 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 aren not related in a simple way. whole: 0.39 (0.21), residues: 1636 helix: 1.98 (0.22), residues: 523 sheet: -0.80 (0.28), residues: 286 loop : -0.43 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 320 TYR 0.020 0.001 TYR E 300 PHE 0.010 0.001 PHE E 737 TRP 0.020 0.001 TRP H 36 HIS 0.004 0.001 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00342 (13701) covalent geometry : angle 0.62633 (18580) hydrogen bonds : bond 0.03647 ( 559) hydrogen bonds : angle 4.39318 ( 1648) metal coordination : bond 0.00139 ( 4) link_ALPHA1-3 : bond 0.01826 ( 2) link_ALPHA1-3 : angle 2.14732 ( 6) link_ALPHA1-6 : bond 0.00579 ( 2) link_ALPHA1-6 : angle 1.66710 ( 6) link_BETA1-4 : bond 0.00666 ( 10) link_BETA1-4 : angle 2.33031 ( 30) link_NAG-ASN : bond 0.00343 ( 6) link_NAG-ASN : angle 1.52975 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.533 Fit side-chains REVERT: A 68 GLU cc_start: 0.7978 (tp30) cc_final: 0.7718 (mp0) REVERT: A 276 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7929 (mm-30) REVERT: A 285 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: A 334 THR cc_start: 0.9084 (m) cc_final: 0.8767 (p) REVERT: A 495 GLU cc_start: 0.8795 (pp20) cc_final: 0.8561 (pp20) REVERT: A 537 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.8108 (t80) REVERT: A 616 MET cc_start: 0.9167 (tpp) cc_final: 0.8928 (tpp) REVERT: A 623 LYS cc_start: 0.9237 (ttpp) cc_final: 0.8721 (pttm) REVERT: A 648 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8102 (tm-30) REVERT: A 651 GLN cc_start: 0.8485 (mm-40) cc_final: 0.7857 (mp10) REVERT: A 653 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7122 (p90) REVERT: A 663 MET cc_start: 0.7787 (mtp) cc_final: 0.7395 (mtm) REVERT: E 109 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8525 (mm-30) REVERT: E 110 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8897 (mp) REVERT: E 285 GLU cc_start: 0.8677 (tm-30) cc_final: 0.7954 (tm-30) REVERT: E 324 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8824 (tmmt) REVERT: E 537 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8101 (t80) REVERT: E 651 GLN cc_start: 0.8483 (mp10) cc_final: 0.8083 (mp10) REVERT: E 663 MET cc_start: 0.7819 (mtp) cc_final: 0.7404 (mtm) REVERT: H 95 TYR cc_start: 0.8543 (m-80) cc_final: 0.7756 (m-10) REVERT: Q 64 LYS cc_start: 0.8670 (ptmm) cc_final: 0.8301 (ptmt) REVERT: Q 95 TYR cc_start: 0.8351 (m-80) cc_final: 0.7735 (m-10) outliers start: 33 outliers final: 13 residues processed: 159 average time/residue: 0.5894 time to fit residues: 103.3882 Evaluate side-chains 151 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain E residue 591 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 9 optimal weight: 0.0060 chunk 74 optimal weight: 0.4980 chunk 96 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.071447 restraints weight = 65105.239| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.00 r_work: 0.2792 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13725 Z= 0.138 Angle : 0.646 13.943 18640 Z= 0.313 Chirality : 0.043 0.196 2009 Planarity : 0.004 0.047 2390 Dihedral : 7.530 81.082 2384 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.66 % Allowed : 21.18 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 aren not related in a simple way. whole: 0.38 (0.21), residues: 1636 helix: 1.96 (0.22), residues: 523 sheet: -0.76 (0.28), residues: 286 loop : -0.44 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 320 TYR 0.022 0.001 TYR E 300 PHE 0.010 0.001 PHE E 737 TRP 0.020 0.001 TRP H 36 HIS 0.004 0.001 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00325 (13701) covalent geometry : angle 0.63692 (18580) hydrogen bonds : bond 0.03605 ( 559) hydrogen bonds : angle 4.38373 ( 1648) metal coordination : bond 0.00117 ( 4) link_ALPHA1-3 : bond 0.01840 ( 2) link_ALPHA1-3 : angle 2.25511 ( 6) link_ALPHA1-6 : bond 0.00571 ( 2) link_ALPHA1-6 : angle 1.67382 ( 6) link_BETA1-4 : bond 0.00659 ( 10) link_BETA1-4 : angle 2.33472 ( 30) link_NAG-ASN : bond 0.00366 ( 6) link_NAG-ASN : angle 1.49469 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.636 Fit side-chains REVERT: A 68 GLU cc_start: 0.8000 (tp30) cc_final: 0.7752 (mp0) REVERT: A 285 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: A 324 LYS cc_start: 0.8689 (tptp) cc_final: 0.8350 (ttmm) REVERT: A 334 THR cc_start: 0.9108 (m) cc_final: 0.8807 (p) REVERT: A 495 GLU cc_start: 0.8797 (pp20) cc_final: 0.8557 (pp20) REVERT: A 537 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.8110 (t80) REVERT: A 563 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8656 (tm-30) REVERT: A 616 MET cc_start: 0.9204 (tpp) cc_final: 0.8959 (tpp) REVERT: A 648 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8113 (tm-30) REVERT: A 651 GLN cc_start: 0.8469 (mm-40) cc_final: 0.7837 (mp10) REVERT: A 653 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.7068 (p90) REVERT: A 663 MET cc_start: 0.7796 (mtp) cc_final: 0.7394 (mtm) REVERT: A 704 SER cc_start: 0.8647 (OUTLIER) cc_final: 0.8322 (m) REVERT: E 109 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8544 (mm-30) REVERT: E 110 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8894 (mp) REVERT: E 285 GLU cc_start: 0.8674 (tm-30) cc_final: 0.7951 (tm-30) REVERT: E 324 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8804 (tmmt) REVERT: E 537 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8184 (t80) REVERT: E 651 GLN cc_start: 0.8527 (mp10) cc_final: 0.8091 (mp10) REVERT: E 663 MET cc_start: 0.7831 (mtp) cc_final: 0.7417 (mtm) REVERT: H 95 TYR cc_start: 0.8577 (m-80) cc_final: 0.7799 (m-10) REVERT: Q 95 TYR cc_start: 0.8366 (m-80) cc_final: 0.7722 (m-10) REVERT: Q 100 ARG cc_start: 0.8609 (mmm160) cc_final: 0.8277 (mmm-85) outliers start: 23 outliers final: 12 residues processed: 157 average time/residue: 0.6202 time to fit residues: 106.7229 Evaluate side-chains 152 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain Q residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 159 optimal weight: 30.0000 chunk 51 optimal weight: 0.0020 chunk 78 optimal weight: 0.0060 chunk 117 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN H 77 ASN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.105569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.072402 restraints weight = 74264.468| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 4.21 r_work: 0.2806 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13725 Z= 0.121 Angle : 0.646 15.308 18640 Z= 0.310 Chirality : 0.042 0.200 2009 Planarity : 0.004 0.054 2390 Dihedral : 7.310 79.669 2384 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.51 % Allowed : 21.76 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 aren not related in a simple way. whole: 0.45 (0.21), residues: 1636 helix: 2.03 (0.22), residues: 523 sheet: -0.72 (0.28), residues: 286 loop : -0.41 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 320 TYR 0.020 0.001 TYR E 300 PHE 0.010 0.001 PHE E 737 TRP 0.021 0.001 TRP H 36 HIS 0.004 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00284 (13701) covalent geometry : angle 0.63625 (18580) hydrogen bonds : bond 0.03441 ( 559) hydrogen bonds : angle 4.32599 ( 1648) metal coordination : bond 0.00077 ( 4) link_ALPHA1-3 : bond 0.01893 ( 2) link_ALPHA1-3 : angle 2.35797 ( 6) link_ALPHA1-6 : bond 0.00569 ( 2) link_ALPHA1-6 : angle 1.66084 ( 6) link_BETA1-4 : bond 0.00670 ( 10) link_BETA1-4 : angle 2.31784 ( 30) link_NAG-ASN : bond 0.00376 ( 6) link_NAG-ASN : angle 1.48980 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.554 Fit side-chains REVERT: A 68 GLU cc_start: 0.7962 (tp30) cc_final: 0.7727 (mp0) REVERT: A 285 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: A 324 LYS cc_start: 0.8713 (tptp) cc_final: 0.8339 (ttmm) REVERT: A 334 THR cc_start: 0.9082 (m) cc_final: 0.8778 (p) REVERT: A 495 GLU cc_start: 0.8763 (pp20) cc_final: 0.8526 (pp20) REVERT: A 537 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8031 (t80) REVERT: A 564 LYS cc_start: 0.9000 (mttm) cc_final: 0.8708 (mttp) REVERT: A 616 MET cc_start: 0.9163 (tpp) cc_final: 0.8909 (tpp) REVERT: A 648 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8047 (tm-30) REVERT: A 651 GLN cc_start: 0.8421 (mm-40) cc_final: 0.7770 (mp10) REVERT: A 653 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6764 (p90) REVERT: A 663 MET cc_start: 0.7683 (mtp) cc_final: 0.7266 (mtm) REVERT: A 704 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.8270 (m) REVERT: E 109 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8514 (mm-30) REVERT: E 285 GLU cc_start: 0.8708 (tm-30) cc_final: 0.7977 (tm-30) REVERT: E 324 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8778 (tmmt) REVERT: E 537 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.8073 (t80) REVERT: E 563 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8642 (tm-30) REVERT: E 651 GLN cc_start: 0.8516 (mp10) cc_final: 0.8085 (mp10) REVERT: E 663 MET cc_start: 0.7777 (mtp) cc_final: 0.7358 (mtm) REVERT: H 95 TYR cc_start: 0.8506 (m-80) cc_final: 0.7603 (m-10) REVERT: Q 95 TYR cc_start: 0.8360 (m-80) cc_final: 0.7729 (m-10) REVERT: Q 100 ARG cc_start: 0.8588 (mmm160) cc_final: 0.8253 (mmm-85) outliers start: 21 outliers final: 12 residues processed: 153 average time/residue: 0.5596 time to fit residues: 94.0361 Evaluate side-chains 153 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain Q residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 88 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 53 optimal weight: 0.0070 chunk 157 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.071364 restraints weight = 56772.278| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.75 r_work: 0.2789 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13725 Z= 0.163 Angle : 0.672 15.045 18640 Z= 0.324 Chirality : 0.044 0.198 2009 Planarity : 0.004 0.055 2390 Dihedral : 7.292 79.694 2384 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.59 % Allowed : 21.69 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 aren not related in a simple way. whole: 0.38 (0.21), residues: 1636 helix: 1.95 (0.22), residues: 521 sheet: -0.78 (0.28), residues: 286 loop : -0.42 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 320 TYR 0.027 0.001 TYR E 300 PHE 0.010 0.001 PHE E 737 TRP 0.022 0.001 TRP H 36 HIS 0.004 0.001 HIS E 377 Details of bonding type rmsd covalent geometry : bond 0.00385 (13701) covalent geometry : angle 0.66271 (18580) hydrogen bonds : bond 0.03804 ( 559) hydrogen bonds : angle 4.41321 ( 1648) metal coordination : bond 0.00174 ( 4) link_ALPHA1-3 : bond 0.01835 ( 2) link_ALPHA1-3 : angle 2.37869 ( 6) link_ALPHA1-6 : bond 0.00554 ( 2) link_ALPHA1-6 : angle 1.74672 ( 6) link_BETA1-4 : bond 0.00642 ( 10) link_BETA1-4 : angle 2.36200 ( 30) link_NAG-ASN : bond 0.00328 ( 6) link_NAG-ASN : angle 1.51012 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5272.28 seconds wall clock time: 90 minutes 31.39 seconds (5431.39 seconds total)