Starting phenix.real_space_refine on Fri Jul 3 10:38:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvi_52435/07_2026/9hvi_52435.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvi_52435/07_2026/9hvi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9hvi_52435/07_2026/9hvi_52435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvi_52435/07_2026/9hvi_52435.map" model { file = "/net/cci-nas-00/data/ceres_data/9hvi_52435/07_2026/9hvi_52435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvi_52435/07_2026/9hvi_52435.cif" } 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-dev-6108/lib/python3.11/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, 58 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 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, 58 Ad-hoc single atom residues: {' CA': 1, ' CL': 1} Unusual residues: {' ZN': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 2 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: 4.05, per 1000 atoms: 0.30 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: 1.25 Conformation dependent library (CDL) restraints added in 641.6 milliseconds 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: 0.34 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: 2.42 Time building geometry restraints manager: 1.57 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: 1.080 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.630 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:8.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 are 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/Z covalent geometry : bond 0.00396 / 0.19 (13701) covalent geometry : angle 0.69539 / 0.35 (18580) hydrogen bonds : bond 0.13920 / 8.80 ( 559) hydrogen bonds : angle 5.82621 / 4.17 ( 1648) metal coordination : bond 0.00146 / 0.07 ( 4) link_ALPHA1-3 : bond 0.00805 / 0.39 ( 2) link_ALPHA1-3 : angle 1.48034 / 1.25 ( 6) link_ALPHA1-6 : bond 0.00522 / 0.26 ( 2) link_ALPHA1-6 : angle 1.65589 / 1.45 ( 6) link_BETA1-4 : bond 0.00688 / 0.43 ( 10) link_BETA1-4 : angle 2.01449 / 1.48 ( 30) link_NAG-ASN : bond 0.00337 / 0.21 ( 6) link_NAG-ASN : angle 1.64690 / 1.13 ( 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 : 0.495 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 189 GLU cc_start: 0.8053 (pp20) cc_final: 0.7722 (pm20) 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: 0.4385 time to fit residues: 136.7607 Evaluate side-chains 178 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3577 r_free = 0.3577 target = 0.107198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.074861 restraints weight = 55731.533| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.82 r_work: 0.2858 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 13725 Z= 0.252 Angle : 0.792 10.886 18640 Z= 0.398 Chirality : 0.049 0.187 2009 Planarity : 0.005 0.055 2390 Dihedral : 10.806 91.663 2392 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.67 % Allowed : 18.16 % Favored : 78.17 % 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 are not related in a simple way. whole: -0.16 (0.20), residues: 1636 helix: 1.17 (0.22), residues: 523 sheet: -0.95 (0.28), residues: 300 loop : -0.53 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 400 TYR 0.035 0.003 TYR H 95 PHE 0.017 0.002 PHE E 546 TRP 0.016 0.002 TRP H 36 HIS 0.009 0.002 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.25 (13701) covalent geometry : angle 0.77923 / 0.40 (18580) hydrogen bonds : bond 0.04802 / 3.22 ( 559) hydrogen bonds : angle 4.86879 / 3.49 ( 1648) metal coordination : bond 0.00309 / 0.16 ( 4) link_ALPHA1-3 : bond 0.00854 / 0.42 ( 2) link_ALPHA1-3 : angle 2.23372 / 1.59 ( 6) link_ALPHA1-6 : bond 0.00838 / 0.43 ( 2) link_ALPHA1-6 : angle 2.95961 / 2.60 ( 6) link_BETA1-4 : bond 0.00913 / 0.58 ( 10) link_BETA1-4 : angle 2.72379 / 2.01 ( 30) link_NAG-ASN : bond 0.00285 / 0.17 ( 6) link_NAG-ASN : angle 2.38536 / 1.65 ( 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 231 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8754 (t70) cc_final: 0.8134 (m-30) REVERT: A 64 GLU cc_start: 0.8777 (tp30) cc_final: 0.8385 (tp30) REVERT: A 68 GLU cc_start: 0.8154 (tp30) cc_final: 0.7845 (OUTLIER) REVERT: A 285 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: A 495 GLU cc_start: 0.8856 (pp20) cc_final: 0.8638 (pp20) REVERT: A 563 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8481 (tm-30) REVERT: A 623 LYS cc_start: 0.9175 (ttpp) cc_final: 0.8753 (pttm) REVERT: A 653 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.6977 (p90) REVERT: E 63 ASP cc_start: 0.8731 (t70) cc_final: 0.8100 (m-30) REVERT: E 64 GLU cc_start: 0.8554 (tp30) cc_final: 0.8049 (tp30) REVERT: E 66 LYS cc_start: 0.8517 (mtmm) cc_final: 0.7702 (mptp) REVERT: E 68 GLU cc_start: 0.8167 (tp30) cc_final: 0.7814 (OUTLIER) REVERT: E 102 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8200 (tm-30) REVERT: E 188 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8501 (mp) REVERT: E 495 GLU cc_start: 0.9005 (pt0) cc_final: 0.8684 (pp20) REVERT: E 563 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8490 (tm-30) REVERT: E 623 LYS cc_start: 0.9173 (ttpp) cc_final: 0.8718 (pttm) REVERT: E 651 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7940 (mm110) REVERT: H 82 GLN cc_start: 0.7975 (tp40) cc_final: 0.7555 (tp-100) REVERT: H 95 TYR cc_start: 0.8120 (m-80) cc_final: 0.7671 (m-10) REVERT: H 99 ARG cc_start: 0.8466 (ptm-80) cc_final: 0.7708 (ptm-80) REVERT: Q 82 GLN cc_start: 0.8190 (tp40) cc_final: 0.7766 (tp-100) REVERT: Q 95 TYR cc_start: 0.8221 (m-10) cc_final: 0.7918 (m-10) REVERT: Q 100 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8430 (mtp180) outliers start: 51 outliers final: 18 residues processed: 215 average time/residue: 0.5276 time to fit residues: 124.5989 Evaluate side-chains 164 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 325 VAL 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 109 GLU 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 486 GLU Chi-restraints excluded: chain E residue 651 GLN 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: 5.9990 chunk 120 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 254 GLN E 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.106424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.073967 restraints weight = 60483.321| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.92 r_work: 0.2821 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13725 Z= 0.150 Angle : 0.632 10.535 18640 Z= 0.310 Chirality : 0.043 0.161 2009 Planarity : 0.004 0.044 2390 Dihedral : 9.654 89.058 2384 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.81 % Allowed : 19.60 % 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 are not related in a simple way. whole: 0.22 (0.21), residues: 1636 helix: 1.72 (0.22), residues: 521 sheet: -0.82 (0.28), residues: 286 loop : -0.47 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 320 TYR 0.026 0.002 TYR E 700 PHE 0.015 0.001 PHE E 506 TRP 0.012 0.001 TRP H 36 HIS 0.004 0.001 HIS E 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (13701) covalent geometry : angle 0.62202 / 0.31 (18580) hydrogen bonds : bond 0.04079 / 2.68 ( 559) hydrogen bonds : angle 4.57474 / 3.29 ( 1648) metal coordination : bond 0.00274 / 0.14 ( 4) link_ALPHA1-3 : bond 0.01750 / 0.87 ( 2) link_ALPHA1-3 : angle 1.85174 / 1.51 ( 6) link_ALPHA1-6 : bond 0.01005 / 0.52 ( 2) link_ALPHA1-6 : angle 1.99570 / 1.41 ( 6) link_BETA1-4 : bond 0.00709 / 0.49 ( 10) link_BETA1-4 : angle 2.33333 / 1.82 ( 30) link_NAG-ASN : bond 0.00331 / 0.19 ( 6) link_NAG-ASN : angle 1.78050 / 1.24 ( 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 184 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8679 (tp30) cc_final: 0.8318 (tp30) REVERT: A 68 GLU cc_start: 0.8068 (tp30) cc_final: 0.7750 (mp0) REVERT: A 285 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: A 495 GLU cc_start: 0.8843 (pp20) cc_final: 0.8622 (pp20) REVERT: A 537 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.7910 (t80) REVERT: A 563 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 616 MET cc_start: 0.9133 (tpp) cc_final: 0.8768 (tpp) REVERT: A 623 LYS cc_start: 0.9168 (ttpp) cc_final: 0.8776 (pttm) REVERT: E 63 ASP cc_start: 0.8722 (t70) cc_final: 0.8049 (m-30) REVERT: E 64 GLU cc_start: 0.8552 (tp30) cc_final: 0.8066 (tp30) REVERT: E 66 LYS cc_start: 0.8568 (mtmm) cc_final: 0.7843 (mptp) REVERT: E 68 GLU cc_start: 0.8029 (tp30) cc_final: 0.7724 (mp0) REVERT: E 102 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8369 (tm-30) REVERT: E 188 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8538 (mp) REVERT: E 495 GLU cc_start: 0.8999 (pt0) cc_final: 0.8564 (pp20) REVERT: E 537 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7792 (t80) REVERT: E 616 MET cc_start: 0.9097 (tpp) cc_final: 0.8736 (tpp) REVERT: E 623 LYS cc_start: 0.9162 (ttpp) cc_final: 0.8729 (pttp) REVERT: E 653 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6777 (p90) REVERT: E 663 MET cc_start: 0.7700 (mtp) cc_final: 0.7281 (mtm) REVERT: E 664 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8257 (mmm) REVERT: H 3 GLN cc_start: 0.7857 (tp40) cc_final: 0.7626 (tp40) REVERT: H 82 GLN cc_start: 0.7965 (tp40) cc_final: 0.7588 (tp-100) REVERT: H 95 TYR cc_start: 0.8473 (m-80) cc_final: 0.7804 (m-10) REVERT: Q 64 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8452 (ptmt) REVERT: Q 82 GLN cc_start: 0.8112 (tp40) cc_final: 0.7702 (tp-100) REVERT: Q 95 TYR cc_start: 0.8251 (m-10) cc_final: 0.7905 (m-10) outliers start: 39 outliers final: 9 residues processed: 172 average time/residue: 0.5468 time to fit residues: 103.2717 Evaluate side-chains 153 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 285 GLU 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 749 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 396 HIS Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain E residue 653 PHE Chi-restraints excluded: chain E residue 664 MET Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 64 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 122 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.071090 restraints weight = 61160.795| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.95 r_work: 0.2770 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 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 = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13725 Z= 0.190 Angle : 0.660 12.022 18640 Z= 0.325 Chirality : 0.045 0.173 2009 Planarity : 0.004 0.045 2390 Dihedral : 8.715 85.708 2383 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.52 % Allowed : 19.02 % Favored : 78.46 % 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 are not related in a simple way. whole: 0.16 (0.21), residues: 1636 helix: 1.75 (0.23), residues: 521 sheet: -0.88 (0.28), residues: 286 loop : -0.55 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 320 TYR 0.037 0.002 TYR E 300 PHE 0.014 0.002 PHE E 546 TRP 0.017 0.001 TRP H 36 HIS 0.006 0.001 HIS E 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (13701) covalent geometry : angle 0.64983 / 0.32 (18580) hydrogen bonds : bond 0.04196 / 2.77 ( 559) hydrogen bonds : angle 4.58189 / 3.29 ( 1648) metal coordination : bond 0.00186 / 0.10 ( 4) link_ALPHA1-3 : bond 0.01568 / 0.78 ( 2) link_ALPHA1-3 : angle 1.90997 / 1.53 ( 6) link_ALPHA1-6 : bond 0.00775 / 0.40 ( 2) link_ALPHA1-6 : angle 1.79052 / 1.42 ( 6) link_BETA1-4 : bond 0.00703 / 0.46 ( 10) link_BETA1-4 : angle 2.45931 / 1.85 ( 30) link_NAG-ASN : bond 0.00271 / 0.16 ( 6) link_NAG-ASN : angle 1.68322 / 1.16 ( 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 174 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8736 (tp30) cc_final: 0.8236 (tp30) REVERT: A 68 GLU cc_start: 0.8040 (tp30) cc_final: 0.7717 (mp0) REVERT: A 495 GLU cc_start: 0.8813 (pp20) cc_final: 0.8577 (pp20) REVERT: A 511 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8227 (ttt90) REVERT: A 537 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8175 (t80) REVERT: A 616 MET cc_start: 0.9224 (tpp) cc_final: 0.8840 (tpp) REVERT: A 651 GLN cc_start: 0.8461 (mm110) cc_final: 0.7737 (mp10) REVERT: A 653 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.7420 (p90) REVERT: A 663 MET cc_start: 0.7737 (mtp) cc_final: 0.7372 (mtm) REVERT: E 64 GLU cc_start: 0.8649 (tp30) cc_final: 0.8392 (tp30) REVERT: E 68 GLU cc_start: 0.8026 (tp30) cc_final: 0.7727 (mp0) REVERT: E 188 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8601 (mp) REVERT: E 285 GLU cc_start: 0.8548 (tm-30) cc_final: 0.7839 (tm-30) REVERT: E 511 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8186 (ttt90) REVERT: E 537 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8148 (t80) REVERT: E 616 MET cc_start: 0.9208 (tpp) cc_final: 0.8952 (tpp) REVERT: E 651 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7963 (mp10) REVERT: E 653 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7037 (p90) REVERT: E 749 VAL cc_start: 0.8239 (m) cc_final: 0.8002 (m) REVERT: H 82 GLN cc_start: 0.8037 (tp40) cc_final: 0.7604 (tp-100) REVERT: H 95 TYR cc_start: 0.8491 (m-80) cc_final: 0.7811 (m-10) REVERT: Q 95 TYR cc_start: 0.8287 (m-80) cc_final: 0.7902 (m-10) outliers start: 35 outliers final: 9 residues processed: 164 average time/residue: 0.5297 time to fit residues: 95.2151 Evaluate side-chains 152 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 653 PHE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 219 LEU 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 H residue 79 VAL Chi-restraints excluded: chain Q residue 31 THR 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: 1.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 160 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.073446 restraints weight = 76450.628| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 4.32 r_work: 0.2803 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 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 = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13725 Z= 0.114 Angle : 0.595 11.070 18640 Z= 0.291 Chirality : 0.043 0.185 2009 Planarity : 0.004 0.044 2390 Dihedral : 8.116 84.145 2383 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.23 % Allowed : 19.02 % Favored : 78.75 % 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 are not related in a simple way. whole: 0.40 (0.21), residues: 1636 helix: 1.99 (0.23), residues: 523 sheet: -0.74 (0.28), residues: 286 loop : -0.44 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 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 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (13701) covalent geometry : angle 0.58500 / 0.29 (18580) hydrogen bonds : bond 0.03491 / 2.29 ( 559) hydrogen bonds : angle 4.36056 / 3.12 ( 1648) metal coordination : bond 0.00069 / 0.04 ( 4) link_ALPHA1-3 : bond 0.01881 / 0.93 ( 2) link_ALPHA1-3 : angle 2.08061 / 1.75 ( 6) link_ALPHA1-6 : bond 0.00682 / 0.34 ( 2) link_ALPHA1-6 : angle 1.59535 / 1.28 ( 6) link_BETA1-4 : bond 0.00688 / 0.45 ( 10) link_BETA1-4 : angle 2.26813 / 1.75 ( 30) link_NAG-ASN : bond 0.00428 / 0.25 ( 6) link_NAG-ASN : angle 1.52632 / 1.08 ( 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 178 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.414 Fit side-chains REVERT: A 63 ASP cc_start: 0.8737 (t0) cc_final: 0.8187 (m-30) REVERT: A 68 GLU cc_start: 0.7992 (tp30) cc_final: 0.7715 (mp0) REVERT: A 169 MET cc_start: 0.6742 (mmt) cc_final: 0.6511 (mmm) REVERT: A 285 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: A 334 THR cc_start: 0.9035 (m) cc_final: 0.8688 (p) REVERT: A 495 GLU cc_start: 0.8810 (pp20) cc_final: 0.8595 (pp20) REVERT: A 537 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.8136 (t80) REVERT: A 563 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8668 (tm-30) REVERT: A 616 MET cc_start: 0.9154 (tpp) cc_final: 0.8840 (tpp) REVERT: A 623 LYS cc_start: 0.9179 (ttpp) cc_final: 0.8640 (pttm) REVERT: A 651 GLN cc_start: 0.8460 (mm-40) cc_final: 0.7837 (mp10) REVERT: A 653 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7207 (p90) REVERT: A 663 MET cc_start: 0.7727 (mtp) cc_final: 0.7370 (mtm) REVERT: E 68 GLU cc_start: 0.8007 (tp30) cc_final: 0.7772 (mp0) REVERT: E 188 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8587 (mp) REVERT: E 285 GLU cc_start: 0.8593 (tm-30) cc_final: 0.7871 (tm-30) REVERT: E 324 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8824 (tmmt) REVERT: E 537 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7914 (t80) REVERT: E 563 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8707 (tm-30) REVERT: E 616 MET cc_start: 0.9176 (tpp) cc_final: 0.8937 (tpp) REVERT: E 651 GLN cc_start: 0.8475 (mp10) cc_final: 0.7982 (mp10) REVERT: E 653 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.6998 (p90) REVERT: E 663 MET cc_start: 0.7796 (mtp) cc_final: 0.7371 (mtm) REVERT: H 95 TYR cc_start: 0.8520 (m-80) cc_final: 0.7786 (m-10) REVERT: Q 64 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8595 (ptmt) REVERT: Q 95 TYR cc_start: 0.8314 (m-80) cc_final: 0.7878 (m-10) outliers start: 31 outliers final: 8 residues processed: 168 average time/residue: 0.4737 time to fit residues: 87.6132 Evaluate side-chains 149 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE 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 653 PHE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain E residue 653 PHE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain Q residue 64 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 ASN H 82 GLN Q 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.104623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.071229 restraints weight = 79213.064| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 4.36 r_work: 0.2758 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 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 = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13725 Z= 0.165 Angle : 0.630 11.104 18640 Z= 0.309 Chirality : 0.044 0.173 2009 Planarity : 0.004 0.045 2390 Dihedral : 7.887 82.404 2383 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.88 % Allowed : 19.45 % Favored : 77.67 % 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 are not related in a simple way. whole: 0.37 (0.21), residues: 1636 helix: 1.98 (0.22), residues: 521 sheet: -0.79 (0.28), residues: 286 loop : -0.45 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 320 TYR 0.017 0.001 TYR A 299 PHE 0.013 0.001 PHE E 546 TRP 0.017 0.001 TRP H 36 HIS 0.004 0.001 HIS E 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (13701) covalent geometry : angle 0.62034 / 0.31 (18580) hydrogen bonds : bond 0.03804 / 2.49 ( 559) hydrogen bonds : angle 4.42035 / 3.18 ( 1648) metal coordination : bond 0.00165 / 0.08 ( 4) link_ALPHA1-3 : bond 0.01752 / 0.87 ( 2) link_ALPHA1-3 : angle 2.05046 / 1.72 ( 6) link_ALPHA1-6 : bond 0.00558 / 0.27 ( 2) link_ALPHA1-6 : angle 1.69922 / 1.41 ( 6) link_BETA1-4 : bond 0.00662 / 0.43 ( 10) link_BETA1-4 : angle 2.34234 / 1.78 ( 30) link_NAG-ASN : bond 0.00343 / 0.20 ( 6) link_NAG-ASN : angle 1.55053 / 1.11 ( 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 181 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7999 (tp30) cc_final: 0.7694 (mp0) REVERT: A 276 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7987 (mm-30) REVERT: A 285 GLU cc_start: 0.8573 (tm-30) cc_final: 0.7823 (tm-30) REVERT: A 334 THR cc_start: 0.9062 (m) cc_final: 0.8725 (p) REVERT: A 489 GLU cc_start: 0.8511 (pm20) cc_final: 0.8163 (mp0) REVERT: A 495 GLU cc_start: 0.8797 (pp20) cc_final: 0.8568 (pp20) REVERT: A 537 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.8076 (t80) REVERT: A 616 MET cc_start: 0.9206 (tpp) cc_final: 0.8925 (tpp) REVERT: A 623 LYS cc_start: 0.9189 (ttpp) cc_final: 0.8671 (pttm) REVERT: A 651 GLN cc_start: 0.8530 (mm-40) cc_final: 0.7905 (mp10) REVERT: A 653 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7217 (p90) REVERT: A 663 MET cc_start: 0.7788 (mtp) cc_final: 0.7411 (mtm) REVERT: E 68 GLU cc_start: 0.8023 (tp30) cc_final: 0.7780 (mp0) REVERT: E 109 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8543 (mm-30) REVERT: E 188 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8615 (mp) REVERT: E 285 GLU cc_start: 0.8659 (tm-30) cc_final: 0.7929 (tm-30) REVERT: E 324 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8816 (tmmt) REVERT: E 537 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8103 (t80) REVERT: E 616 MET cc_start: 0.9212 (tpp) cc_final: 0.8932 (tpp) REVERT: E 651 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: E 663 MET cc_start: 0.7819 (mtp) cc_final: 0.7390 (mtm) REVERT: H 82 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7905 (tp40) REVERT: H 95 TYR cc_start: 0.8541 (m-80) cc_final: 0.7727 (m-10) REVERT: Q 95 TYR cc_start: 0.8344 (m-80) cc_final: 0.7868 (m-10) outliers start: 40 outliers final: 16 residues processed: 165 average time/residue: 0.4920 time to fit residues: 89.5304 Evaluate side-chains 159 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 244 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 317 SER 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 537 TYR Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain E residue 591 ILE Chi-restraints excluded: chain E residue 651 GLN Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 56 SER 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: 0.9980 chunk 121 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 ASN H 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.105768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.072445 restraints weight = 75504.986| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.31 r_work: 0.2787 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 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 = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.5639 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= 0.120 Angle : 0.611 11.959 18640 Z= 0.298 Chirality : 0.043 0.165 2009 Planarity : 0.004 0.048 2390 Dihedral : 7.641 80.002 2383 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.23 % Allowed : 20.17 % 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 are not related in a simple way. whole: 0.46 (0.21), residues: 1636 helix: 2.09 (0.22), residues: 521 sheet: -0.75 (0.28), residues: 286 loop : -0.42 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 320 TYR 0.027 0.001 TYR H 29 PHE 0.013 0.001 PHE E 506 TRP 0.016 0.001 TRP H 36 HIS 0.004 0.001 HIS E 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (13701) covalent geometry : angle 0.60129 / 0.30 (18580) hydrogen bonds : bond 0.03485 / 2.29 ( 559) hydrogen bonds : angle 4.32058 / 3.11 ( 1648) metal coordination : bond 0.00074 / 0.04 ( 4) link_ALPHA1-3 : bond 0.01896 / 0.94 ( 2) link_ALPHA1-3 : angle 2.22584 / 1.87 ( 6) link_ALPHA1-6 : bond 0.00703 / 0.35 ( 2) link_ALPHA1-6 : angle 1.68081 / 1.38 ( 6) link_BETA1-4 : bond 0.00706 / 0.44 ( 10) link_BETA1-4 : angle 2.30348 / 1.76 ( 30) link_NAG-ASN : bond 0.00395 / 0.23 ( 6) link_NAG-ASN : angle 1.52396 / 1.09 ( 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 : 0.519 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7960 (tp30) cc_final: 0.7706 (mp0) REVERT: A 169 MET cc_start: 0.6747 (mmt) cc_final: 0.6539 (mmt) REVERT: A 276 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8118 (mm-30) REVERT: A 285 GLU cc_start: 0.8583 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 334 THR cc_start: 0.9057 (m) cc_final: 0.8740 (p) REVERT: A 489 GLU cc_start: 0.8465 (pm20) cc_final: 0.8184 (mp0) REVERT: A 495 GLU cc_start: 0.8784 (pp20) cc_final: 0.8574 (pp20) REVERT: A 537 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.8053 (t80) REVERT: A 563 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8658 (tm-30) REVERT: A 616 MET cc_start: 0.9156 (tpp) cc_final: 0.8915 (tpp) REVERT: A 623 LYS cc_start: 0.9188 (ttpp) cc_final: 0.8695 (pttm) REVERT: A 651 GLN cc_start: 0.8516 (mm-40) cc_final: 0.7908 (mp10) REVERT: A 653 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.7022 (p90) REVERT: A 663 MET cc_start: 0.7809 (mtp) cc_final: 0.7377 (mtm) REVERT: A 673 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8972 (tpp-160) REVERT: E 68 GLU cc_start: 0.8001 (tp30) cc_final: 0.7795 (mp0) REVERT: E 109 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8553 (mm-30) REVERT: E 188 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8594 (mp) REVERT: E 285 GLU cc_start: 0.8671 (tm-30) cc_final: 0.7951 (tm-30) REVERT: E 324 LYS cc_start: 0.9041 (ttmm) cc_final: 0.8794 (tmmt) REVERT: E 537 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8084 (t80) REVERT: E 563 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8683 (tm-30) REVERT: E 616 MET cc_start: 0.9186 (tpp) cc_final: 0.8943 (tpp) REVERT: E 651 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8016 (mp10) REVERT: E 663 MET cc_start: 0.7809 (mtp) cc_final: 0.7403 (mtm) REVERT: H 82 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.8037 (tp40) REVERT: H 95 TYR cc_start: 0.8536 (m-80) cc_final: 0.7736 (m-10) REVERT: Q 95 TYR cc_start: 0.8355 (m-80) cc_final: 0.7749 (m-10) outliers start: 31 outliers final: 15 residues processed: 158 average time/residue: 0.5132 time to fit residues: 89.3096 Evaluate side-chains 158 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 219 LEU Chi-restraints excluded: chain A residue 276 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 353 THR 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 673 ARG Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 188 LEU 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 H residue 82 GLN Chi-restraints excluded: chain Q residue 56 SER Chi-restraints excluded: chain Q residue 64 LYS Chi-restraints excluded: chain Q residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 144 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 114 optimal weight: 0.0670 chunk 118 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 ASN H 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.105943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.072649 restraints weight = 70429.125| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.19 r_work: 0.2802 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 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 = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13725 Z= 0.121 Angle : 0.614 12.024 18640 Z= 0.298 Chirality : 0.042 0.159 2009 Planarity : 0.004 0.052 2390 Dihedral : 7.462 78.506 2383 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.59 % Allowed : 19.88 % Favored : 77.52 % 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 are not related in a simple way. whole: 0.50 (0.21), residues: 1636 helix: 2.13 (0.22), residues: 521 sheet: -0.69 (0.28), residues: 286 loop : -0.42 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 320 TYR 0.022 0.001 TYR H 29 PHE 0.012 0.001 PHE E 546 TRP 0.020 0.001 TRP H 36 HIS 0.004 0.001 HIS E 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (13701) covalent geometry : angle 0.60376 / 0.30 (18580) hydrogen bonds : bond 0.03442 / 2.26 ( 559) hydrogen bonds : angle 4.29081 / 3.09 ( 1648) metal coordination : bond 0.00073 / 0.04 ( 4) link_ALPHA1-3 : bond 0.01820 / 0.90 ( 2) link_ALPHA1-3 : angle 2.21598 / 1.86 ( 6) link_ALPHA1-6 : bond 0.00578 / 0.28 ( 2) link_ALPHA1-6 : angle 1.66399 / 1.37 ( 6) link_BETA1-4 : bond 0.00723 / 0.45 ( 10) link_BETA1-4 : angle 2.32078 / 1.77 ( 30) link_NAG-ASN : bond 0.00357 / 0.21 ( 6) link_NAG-ASN : angle 1.51577 / 1.08 ( 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 179 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7955 (tp30) cc_final: 0.7710 (mp0) REVERT: A 169 MET cc_start: 0.6739 (mmt) cc_final: 0.6511 (mmt) REVERT: A 276 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: A 285 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: A 334 THR cc_start: 0.9061 (m) cc_final: 0.8754 (p) REVERT: A 489 GLU cc_start: 0.8455 (pm20) cc_final: 0.8180 (mp0) REVERT: A 495 GLU cc_start: 0.8790 (pp20) cc_final: 0.8572 (pp20) REVERT: A 537 TYR cc_start: 0.8661 (OUTLIER) cc_final: 0.8091 (t80) REVERT: A 616 MET cc_start: 0.9158 (tpp) cc_final: 0.8914 (tpp) REVERT: A 623 LYS cc_start: 0.9195 (ttpp) cc_final: 0.8706 (pttm) REVERT: A 651 GLN cc_start: 0.8526 (mm-40) cc_final: 0.7900 (mp10) REVERT: A 653 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7074 (p90) REVERT: A 663 MET cc_start: 0.7796 (mtp) cc_final: 0.7355 (mtm) REVERT: E 109 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8540 (mm-30) REVERT: E 188 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8590 (mp) REVERT: E 285 GLU cc_start: 0.8699 (tm-30) cc_final: 0.7980 (tm-30) REVERT: E 289 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9314 (mp) REVERT: E 324 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8803 (tmmt) REVERT: E 537 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.8082 (t80) REVERT: E 616 MET cc_start: 0.9183 (tpp) cc_final: 0.8926 (tpp) REVERT: E 651 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: H 95 TYR cc_start: 0.8512 (m-80) cc_final: 0.7736 (m-10) REVERT: Q 95 TYR cc_start: 0.8365 (m-80) cc_final: 0.7753 (m-10) outliers start: 36 outliers final: 16 residues processed: 166 average time/residue: 0.5112 time to fit residues: 93.2358 Evaluate side-chains 161 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 289 LEU 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 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 158 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 289 LEU 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 H residue 22 CYS Chi-restraints excluded: chain Q residue 56 SER Chi-restraints excluded: chain Q residue 64 LYS Chi-restraints excluded: chain Q residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 9 optimal weight: 0.0470 chunk 74 optimal weight: 0.0770 chunk 96 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 145 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 ASN H 82 GLN Q 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.106245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.073202 restraints weight = 65913.301| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.09 r_work: 0.2805 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.5770 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 : 0.621 12.336 18640 Z= 0.301 Chirality : 0.042 0.155 2009 Planarity : 0.004 0.054 2390 Dihedral : 7.291 76.942 2383 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.16 % Allowed : 20.32 % Favored : 77.52 % 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 are not related in a simple way. whole: 0.52 (0.21), residues: 1636 helix: 2.17 (0.22), residues: 521 sheet: -0.66 (0.28), residues: 286 loop : -0.43 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 320 TYR 0.030 0.001 TYR H 29 PHE 0.012 0.001 PHE E 546 TRP 0.019 0.001 TRP H 36 HIS 0.004 0.001 HIS E 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (13701) covalent geometry : angle 0.61094 / 0.30 (18580) hydrogen bonds : bond 0.03364 / 2.21 ( 559) hydrogen bonds : angle 4.28054 / 3.08 ( 1648) metal coordination : bond 0.00049 / 0.02 ( 4) link_ALPHA1-3 : bond 0.01874 / 0.92 ( 2) link_ALPHA1-3 : angle 2.32313 / 1.95 ( 6) link_ALPHA1-6 : bond 0.00552 / 0.27 ( 2) link_ALPHA1-6 : angle 1.65582 / 1.36 ( 6) link_BETA1-4 : bond 0.00702 / 0.43 ( 10) link_BETA1-4 : angle 2.31424 / 1.76 ( 30) link_NAG-ASN : bond 0.00372 / 0.22 ( 6) link_NAG-ASN : angle 1.48864 / 1.06 ( 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 174 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7951 (tp30) cc_final: 0.7711 (mp0) REVERT: A 169 MET cc_start: 0.6697 (mmt) cc_final: 0.6468 (mmt) REVERT: A 181 ARG cc_start: 0.8542 (mtm180) cc_final: 0.8206 (mtm180) REVERT: A 285 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: A 324 LYS cc_start: 0.8655 (tptp) cc_final: 0.8281 (ttmm) REVERT: A 334 THR cc_start: 0.9058 (m) cc_final: 0.8756 (p) REVERT: A 489 GLU cc_start: 0.8456 (pm20) cc_final: 0.8168 (mp0) REVERT: A 495 GLU cc_start: 0.8778 (pp20) cc_final: 0.8560 (pp20) REVERT: A 537 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7990 (t80) REVERT: A 563 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8646 (tm-30) REVERT: A 564 LYS cc_start: 0.9025 (mttm) cc_final: 0.8763 (mttp) REVERT: A 616 MET cc_start: 0.9147 (tpp) cc_final: 0.8908 (tpp) REVERT: A 623 LYS cc_start: 0.9208 (ttpp) cc_final: 0.8724 (pttm) REVERT: A 651 GLN cc_start: 0.8561 (mm-40) cc_final: 0.7960 (mp10) REVERT: A 653 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7082 (p90) REVERT: A 663 MET cc_start: 0.7782 (mtp) cc_final: 0.7332 (mtm) REVERT: E 109 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8524 (mm-30) REVERT: E 188 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8566 (mp) REVERT: E 285 GLU cc_start: 0.8694 (tm-30) cc_final: 0.7979 (tm-30) REVERT: E 289 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9302 (mp) REVERT: E 324 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8798 (tmmt) REVERT: E 537 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.8033 (t80) REVERT: E 563 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8659 (tm-30) REVERT: E 616 MET cc_start: 0.9178 (tpp) cc_final: 0.8924 (tpp) REVERT: E 651 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8072 (mp10) REVERT: E 663 MET cc_start: 0.7707 (mtm) cc_final: 0.7426 (mtm) REVERT: H 95 TYR cc_start: 0.8518 (m-80) cc_final: 0.7739 (m-10) REVERT: Q 95 TYR cc_start: 0.8383 (m-80) cc_final: 0.7689 (m-10) outliers start: 30 outliers final: 16 residues processed: 161 average time/residue: 0.4946 time to fit residues: 87.4319 Evaluate side-chains 162 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 158 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 289 LEU 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 749 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain Q residue 56 SER Chi-restraints excluded: chain Q residue 64 LYS 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: 0.0060 chunk 62 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 51 optimal weight: 0.0470 chunk 78 optimal weight: 0.0670 chunk 117 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 overall best weight: 0.3232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 ASN H 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.108419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.075718 restraints weight = 74621.195| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 4.23 r_work: 0.2853 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13725 Z= 0.110 Angle : 0.618 12.461 18640 Z= 0.300 Chirality : 0.042 0.161 2009 Planarity : 0.004 0.054 2390 Dihedral : 6.980 73.579 2383 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.59 % Allowed : 20.89 % Favored : 77.52 % 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 are not related in a simple way. whole: 0.61 (0.21), residues: 1636 helix: 2.26 (0.22), residues: 521 sheet: -0.62 (0.28), residues: 286 loop : -0.39 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 320 TYR 0.020 0.001 TYR H 29 PHE 0.011 0.001 PHE E 546 TRP 0.021 0.001 TRP H 36 HIS 0.004 0.001 HIS E 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (13701) covalent geometry : angle 0.60854 / 0.30 (18580) hydrogen bonds : bond 0.03158 / 2.09 ( 559) hydrogen bonds : angle 4.21763 / 3.03 ( 1648) metal coordination : bond 0.00010 / 0.01 ( 4) link_ALPHA1-3 : bond 0.01910 / 0.94 ( 2) link_ALPHA1-3 : angle 2.44982 / 2.05 ( 6) link_ALPHA1-6 : bond 0.00546 / 0.27 ( 2) link_ALPHA1-6 : angle 1.63574 / 1.34 ( 6) link_BETA1-4 : bond 0.00698 / 0.43 ( 10) link_BETA1-4 : angle 2.29077 / 1.74 ( 30) link_NAG-ASN : bond 0.00400 / 0.24 ( 6) link_NAG-ASN : angle 1.47002 / 1.04 ( 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 172 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7996 (tp30) cc_final: 0.7786 (mp0) REVERT: A 169 MET cc_start: 0.6608 (mmt) cc_final: 0.6361 (mmt) REVERT: A 285 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: A 324 LYS cc_start: 0.8697 (tptp) cc_final: 0.8331 (ttmm) REVERT: A 351 GLU cc_start: 0.8504 (pt0) cc_final: 0.8284 (pt0) REVERT: A 489 GLU cc_start: 0.8424 (pm20) cc_final: 0.8159 (mp0) REVERT: A 495 GLU cc_start: 0.8775 (pp20) cc_final: 0.8573 (pp20) REVERT: A 537 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8029 (t80) REVERT: A 564 LYS cc_start: 0.9022 (mttm) cc_final: 0.8751 (mttp) REVERT: A 616 MET cc_start: 0.9126 (tpp) cc_final: 0.8907 (tpp) REVERT: A 651 GLN cc_start: 0.8541 (mm-40) cc_final: 0.7899 (mp10) REVERT: A 663 MET cc_start: 0.7854 (mtp) cc_final: 0.7416 (mtm) REVERT: E 109 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8546 (mm-30) REVERT: E 285 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8001 (tm-30) REVERT: E 324 LYS cc_start: 0.9028 (ttmm) cc_final: 0.8796 (tmmt) REVERT: E 537 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7970 (t80) REVERT: E 563 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8651 (tm-30) REVERT: E 616 MET cc_start: 0.9169 (tpp) cc_final: 0.8941 (tpp) REVERT: E 645 LYS cc_start: 0.8625 (mmpt) cc_final: 0.8392 (mmmt) REVERT: E 648 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8085 (tm-30) REVERT: E 651 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8046 (mp10) REVERT: E 663 MET cc_start: 0.7717 (mtm) cc_final: 0.7434 (mtm) REVERT: H 95 TYR cc_start: 0.8553 (m-80) cc_final: 0.7629 (m-10) REVERT: Q 95 TYR cc_start: 0.8419 (m-80) cc_final: 0.7751 (m-10) outliers start: 22 outliers final: 15 residues processed: 161 average time/residue: 0.5031 time to fit residues: 89.1964 Evaluate side-chains 159 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 749 VAL Chi-restraints excluded: chain E residue 158 VAL 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 749 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain Q residue 56 SER Chi-restraints excluded: chain Q residue 64 LYS 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: 1.9990 chunk 11 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 ASN Q 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.103561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.070453 restraints weight = 57572.994| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.88 r_work: 0.2762 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13725 Z= 0.214 Angle : 0.695 12.760 18640 Z= 0.340 Chirality : 0.045 0.217 2009 Planarity : 0.005 0.058 2390 Dihedral : 7.234 75.140 2383 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.80 % Allowed : 21.69 % Favored : 76.51 % 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 are not related in a simple way. whole: 0.33 (0.21), residues: 1636 helix: 1.92 (0.22), residues: 523 sheet: -0.73 (0.28), residues: 284 loop : -0.51 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 320 TYR 0.028 0.002 TYR H 29 PHE 0.015 0.001 PHE E 546 TRP 0.022 0.002 TRP H 36 HIS 0.004 0.001 HIS E 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 (13701) covalent geometry : angle 0.68595 / 0.34 (18580) hydrogen bonds : bond 0.04092 / 2.68 ( 559) hydrogen bonds : angle 4.47988 / 3.24 ( 1648) metal coordination : bond 0.00298 / 0.15 ( 4) link_ALPHA1-3 : bond 0.01802 / 0.88 ( 2) link_ALPHA1-3 : angle 2.41479 / 2.05 ( 6) link_ALPHA1-6 : bond 0.00538 / 0.26 ( 2) link_ALPHA1-6 : angle 1.83184 / 1.56 ( 6) link_BETA1-4 : bond 0.00647 / 0.37 ( 10) link_BETA1-4 : angle 2.40906 / 1.82 ( 30) link_NAG-ASN : bond 0.00302 / 0.18 ( 6) link_NAG-ASN : angle 1.55563 / 1.10 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4889.29 seconds wall clock time: 84 minutes 4.21 seconds (5044.21 seconds total)