Starting phenix.real_space_refine on Thu Jul 31 18:00:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvi_52435/07_2025/9hvi_52435.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvi_52435/07_2025/9hvi_52435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hvi_52435/07_2025/9hvi_52435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvi_52435/07_2025/9hvi_52435.map" model { file = "/net/cci-nas-00/data/ceres_data/9hvi_52435/07_2025/9hvi_52435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvi_52435/07_2025/9hvi_52435.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13352 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5537 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 650} Chain: "E" Number of atoms: 5550 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 695, 5537 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 650} Conformer: "B" Number of residues, atoms: 695, 5537 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 650} bond proxies already assigned to first conformer: 5679 Chain: "H" Number of atoms: 945 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Conformer: "C" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} bond proxies already assigned to first conformer: 957 Chain: "Q" Number of atoms: 945 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Conformer: "B" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} bond proxies already assigned to first conformer: 957 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Unusual residues: {' CA': 1, ' ZN': 2, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 60 Unusual residues: {' CA': 1, ' CL': 1, ' ZN': 2, 'NAG': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER E 155 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER E 155 " occ=0.50 residue: pdb=" N AVAL E 660 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL E 660 " occ=0.50 Time building chain proxies: 11.87, per 1000 atoms: 0.89 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: 4.15 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.55 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: 4.69 Time building geometry restraints manager: 4.48 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 750 or resid 801 through 807)) selection = (chain 'E' and (resid 56 through 154 or resid 156 through 659 or resid 661 throu \ gh 750 or resid 801 through 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 42.050 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 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:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13725 Z= 0.186 Angle : 0.702 13.172 18640 Z= 0.349 Chirality : 0.046 0.365 2009 Planarity : 0.004 0.055 2390 Dihedral : 16.401 109.308 5460 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.01 % Allowed : 19.67 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.036 0.002 TRP H 36 HIS 0.004 0.001 HIS E 377 PHE 0.017 0.001 PHE A 546 TYR 0.020 0.001 TYR E 300 ARG 0.015 0.001 ARG E 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 6) link_NAG-ASN : angle 1.64690 ( 18) link_ALPHA1-6 : bond 0.00522 ( 2) link_ALPHA1-6 : angle 1.65589 ( 6) link_BETA1-4 : bond 0.00688 ( 10) link_BETA1-4 : angle 2.01449 ( 30) link_ALPHA1-3 : bond 0.00805 ( 2) link_ALPHA1-3 : angle 1.48034 ( 6) hydrogen bonds : bond 0.13920 ( 559) hydrogen bonds : angle 5.82621 ( 1648) metal coordination : bond 0.00146 ( 4) covalent geometry : bond 0.00396 (13701) covalent geometry : angle 0.69539 (18580) *********************** 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 : 1.395 Fit side-chains revert: symmetry clash 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: 0.7336 (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: 0.8323 (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: 1.0587 time to fit residues: 330.7820 Evaluate side-chains 180 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 136 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 328 ASN E 136 ASN E 254 GLN E 303 GLN E 328 ASN H 77 ASN H 82 GLN Q 5 GLN Q 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.105951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.073053 restraints weight = 73354.678| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.25 r_work: 0.2810 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13725 Z= 0.259 Angle : 0.780 10.098 18640 Z= 0.390 Chirality : 0.049 0.197 2009 Planarity : 0.005 0.053 2390 Dihedral : 11.088 93.590 2392 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.89 % Allowed : 18.23 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1636 helix: 1.20 (0.22), residues: 521 sheet: -1.02 (0.28), residues: 300 loop : -0.52 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 36 HIS 0.008 0.002 HIS E 377 PHE 0.017 0.002 PHE E 546 TYR 0.033 0.003 TYR H 95 ARG 0.011 0.001 ARG E 400 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 6) link_NAG-ASN : angle 2.39815 ( 18) link_ALPHA1-6 : bond 0.00764 ( 2) link_ALPHA1-6 : angle 3.11118 ( 6) link_BETA1-4 : bond 0.00774 ( 10) link_BETA1-4 : angle 2.72480 ( 30) link_ALPHA1-3 : bond 0.01170 ( 2) link_ALPHA1-3 : angle 2.40399 ( 6) hydrogen bonds : bond 0.04903 ( 559) hydrogen bonds : angle 4.85842 ( 1648) metal coordination : bond 0.01336 ( 4) covalent geometry : bond 0.00597 (13701) covalent geometry : angle 0.76691 (18580) *********************** 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 232 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 178 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8771 (t70) cc_final: 0.8169 (m-30) REVERT: A 64 GLU cc_start: 0.8756 (tp30) cc_final: 0.8364 (tp30) REVERT: A 285 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: A 495 GLU cc_start: 0.8848 (pp20) cc_final: 0.8637 (pp20) REVERT: A 563 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8541 (tm-30) REVERT: A 623 LYS cc_start: 0.9181 (ttpp) cc_final: 0.8719 (pttm) REVERT: E 63 ASP cc_start: 0.8747 (t70) cc_final: 0.7989 (m-30) REVERT: E 64 GLU cc_start: 0.8575 (tp30) cc_final: 0.8048 (tp30) REVERT: E 66 LYS cc_start: 0.8533 (mtmm) cc_final: 0.7680 (mptp) REVERT: E 68 GLU cc_start: 0.8203 (tp30) cc_final: 0.7817 (OUTLIER) REVERT: E 102 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8281 (tm-30) REVERT: E 188 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8521 (mp) REVERT: E 300 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7705 (t80) REVERT: E 495 GLU cc_start: 0.9021 (pt0) cc_final: 0.8656 (pp20) REVERT: E 563 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8525 (tm-30) REVERT: E 616 MET cc_start: 0.9080 (tpp) cc_final: 0.8847 (mmm) REVERT: E 623 LYS cc_start: 0.9173 (ttpp) cc_final: 0.8721 (pttm) REVERT: H 82 GLN cc_start: 0.7918 (tp40) cc_final: 0.7492 (tp-100) REVERT: H 95 TYR cc_start: 0.8124 (m-80) cc_final: 0.7678 (m-10) REVERT: H 99 ARG cc_start: 0.8497 (ptm-80) cc_final: 0.7650 (ptm-80) REVERT: Q 64 LYS cc_start: 0.8621 (mtpm) cc_final: 0.8286 (ptmt) REVERT: Q 82 GLN cc_start: 0.8116 (tp40) cc_final: 0.7735 (tp-100) REVERT: Q 95 TYR cc_start: 0.8186 (m-10) cc_final: 0.7923 (m-10) REVERT: Q 100 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8397 (mtp180) REVERT: Q 101 ASP cc_start: 0.8049 (t0) cc_final: 0.7805 (t0) outliers start: 54 outliers final: 16 residues processed: 216 average time/residue: 1.1733 time to fit residues: 278.5316 Evaluate side-chains 160 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 325 VAL Chi-restraints excluded: chain A residue 396 HIS 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 H residue 56 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain Q residue 31 THR 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 80 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 83 optimal weight: 0.3980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 GLN E 254 GLN E 340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.106468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.073647 restraints weight = 72209.368| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.20 r_work: 0.2807 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- 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 = 0.47 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 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13725 Z= 0.143 Angle : 0.625 11.290 18640 Z= 0.307 Chirality : 0.043 0.153 2009 Planarity : 0.004 0.044 2390 Dihedral : 9.816 88.260 2385 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.88 % Allowed : 19.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1636 helix: 1.71 (0.22), residues: 523 sheet: -0.94 (0.27), residues: 308 loop : -0.41 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.004 0.001 HIS E 82 PHE 0.016 0.001 PHE E 506 TYR 0.018 0.001 TYR H 29 ARG 0.012 0.001 ARG E 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 6) link_NAG-ASN : angle 1.76874 ( 18) link_ALPHA1-6 : bond 0.01021 ( 2) link_ALPHA1-6 : angle 2.09742 ( 6) link_BETA1-4 : bond 0.00698 ( 10) link_BETA1-4 : angle 2.35054 ( 30) link_ALPHA1-3 : bond 0.01684 ( 2) link_ALPHA1-3 : angle 1.76573 ( 6) hydrogen bonds : bond 0.03945 ( 559) hydrogen bonds : angle 4.56749 ( 1648) metal coordination : bond 0.00431 ( 4) covalent geometry : bond 0.00326 (13701) covalent geometry : angle 0.61411 (18580) *********************** 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 185 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8676 (tp30) cc_final: 0.8283 (tp30) REVERT: A 68 GLU cc_start: 0.8085 (tp30) cc_final: 0.7757 (mp0) REVERT: A 285 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: A 495 GLU cc_start: 0.8863 (pp20) cc_final: 0.8648 (pp20) REVERT: A 537 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7835 (t80) REVERT: A 563 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8662 (tm-30) REVERT: A 616 MET cc_start: 0.9143 (tpp) cc_final: 0.8767 (tpp) REVERT: A 623 LYS cc_start: 0.9171 (ttpp) cc_final: 0.8773 (pttm) REVERT: A 651 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7604 (mp10) REVERT: A 653 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.6977 (p90) REVERT: E 63 ASP cc_start: 0.8762 (t70) cc_final: 0.8086 (m-30) REVERT: E 64 GLU cc_start: 0.8552 (tp30) cc_final: 0.8062 (tp30) REVERT: E 66 LYS cc_start: 0.8575 (mtmm) cc_final: 0.7828 (mptp) REVERT: E 68 GLU cc_start: 0.8052 (tp30) cc_final: 0.7726 (mp0) REVERT: E 102 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8378 (tm-30) REVERT: E 188 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8576 (mp) REVERT: E 300 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7593 (t80) REVERT: E 495 GLU cc_start: 0.9003 (pt0) cc_final: 0.8527 (pp20) REVERT: E 537 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7843 (t80) REVERT: E 616 MET cc_start: 0.9121 (tpp) cc_final: 0.8852 (tpp) REVERT: E 623 LYS cc_start: 0.9161 (ttpp) cc_final: 0.8718 (pttm) REVERT: E 653 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6758 (p90) REVERT: E 663 MET cc_start: 0.7752 (mtp) cc_final: 0.7393 (mtm) REVERT: E 664 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8246 (mmm) REVERT: H 3 GLN cc_start: 0.7828 (tp40) cc_final: 0.7618 (tp40) REVERT: H 82 GLN cc_start: 0.8007 (tp40) cc_final: 0.7623 (tp-100) REVERT: H 95 TYR cc_start: 0.8419 (m-80) cc_final: 0.7754 (m-10) REVERT: Q 64 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8432 (ptmt) REVERT: Q 82 GLN cc_start: 0.8116 (tp40) cc_final: 0.7761 (tp40) REVERT: Q 83 MET cc_start: 0.8037 (mmt) cc_final: 0.7827 (mpt) REVERT: Q 95 TYR cc_start: 0.8208 (m-10) cc_final: 0.7858 (m-10) REVERT: Q 101 ASP cc_start: 0.7818 (t0) cc_final: 0.7605 (t0) outliers start: 40 outliers final: 10 residues processed: 169 average time/residue: 1.2241 time to fit residues: 227.4081 Evaluate side-chains 155 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 317 SER 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 651 GLN 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 300 TYR 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 651 GLN 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 21 SER 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 75 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 64 optimal weight: 0.0670 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN Q 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.103201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.070259 restraints weight = 56236.105| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.81 r_work: 0.2758 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 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 = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13725 Z= 0.220 Angle : 0.664 10.970 18640 Z= 0.328 Chirality : 0.045 0.177 2009 Planarity : 0.004 0.045 2390 Dihedral : 8.998 86.744 2383 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.31 % Allowed : 18.73 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1636 helix: 1.63 (0.22), residues: 521 sheet: -1.03 (0.27), residues: 308 loop : -0.49 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.006 0.001 HIS E 377 PHE 0.015 0.002 PHE E 546 TYR 0.022 0.002 TYR E 300 ARG 0.006 0.001 ARG E 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 6) link_NAG-ASN : angle 1.74578 ( 18) link_ALPHA1-6 : bond 0.00743 ( 2) link_ALPHA1-6 : angle 1.81715 ( 6) link_BETA1-4 : bond 0.00696 ( 10) link_BETA1-4 : angle 2.47536 ( 30) link_ALPHA1-3 : bond 0.01386 ( 2) link_ALPHA1-3 : angle 1.77348 ( 6) hydrogen bonds : bond 0.04401 ( 559) hydrogen bonds : angle 4.62663 ( 1648) metal coordination : bond 0.00222 ( 4) covalent geometry : bond 0.00515 (13701) covalent geometry : angle 0.65327 (18580) *********************** 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 183 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 1.386 Fit side-chains REVERT: A 68 GLU cc_start: 0.8036 (tp30) cc_final: 0.7691 (mp0) REVERT: A 181 ARG cc_start: 0.8534 (mtm180) cc_final: 0.8224 (mtm180) REVERT: A 495 GLU cc_start: 0.8799 (pp20) cc_final: 0.8569 (pp20) REVERT: A 511 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8257 (ttt90) REVERT: A 537 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.8181 (t80) REVERT: A 616 MET cc_start: 0.9225 (tpp) cc_final: 0.8816 (tpp) REVERT: A 648 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8272 (mt-10) REVERT: A 651 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7715 (mp10) REVERT: A 673 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8974 (tpp-160) REVERT: E 63 ASP cc_start: 0.8737 (t70) cc_final: 0.8174 (m-30) REVERT: E 68 GLU cc_start: 0.8043 (tp30) cc_final: 0.7738 (mp0) REVERT: E 188 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8596 (mp) REVERT: E 285 GLU cc_start: 0.8517 (tm-30) cc_final: 0.7792 (tm-30) REVERT: E 511 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8182 (ttt90) REVERT: E 537 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8126 (t80) REVERT: E 616 MET cc_start: 0.9209 (tpp) cc_final: 0.8952 (tpp) REVERT: E 651 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: E 653 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7113 (p90) REVERT: E 749 VAL cc_start: 0.8252 (m) cc_final: 0.8013 (m) REVERT: H 82 GLN cc_start: 0.8084 (tp40) cc_final: 0.7787 (tp40) REVERT: H 95 TYR cc_start: 0.8483 (m-80) cc_final: 0.7862 (m-10) REVERT: Q 82 GLN cc_start: 0.8253 (tp40) cc_final: 0.7810 (tp-100) REVERT: Q 83 MET cc_start: 0.8144 (mmt) cc_final: 0.7888 (mpt) REVERT: Q 95 TYR cc_start: 0.8290 (m-80) cc_final: 0.7921 (m-10) outliers start: 46 outliers final: 10 residues processed: 165 average time/residue: 1.1655 time to fit residues: 211.9952 Evaluate side-chains 152 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 651 GLN 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 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 Q residue 33 SER 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 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN ** Q 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.105450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.072558 restraints weight = 63746.578| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 4.01 r_work: 0.2790 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- 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 = 0.49 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 = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13725 Z= 0.122 Angle : 0.606 10.978 18640 Z= 0.296 Chirality : 0.043 0.181 2009 Planarity : 0.004 0.044 2390 Dihedral : 8.413 83.925 2383 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.67 % Allowed : 18.95 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1636 helix: 1.87 (0.23), residues: 523 sheet: -0.86 (0.28), residues: 286 loop : -0.49 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 36 HIS 0.004 0.001 HIS E 82 PHE 0.019 0.001 PHE Q 68 TYR 0.016 0.001 TYR E 300 ARG 0.009 0.000 ARG A 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 6) link_NAG-ASN : angle 1.59172 ( 18) link_ALPHA1-6 : bond 0.00737 ( 2) link_ALPHA1-6 : angle 1.63376 ( 6) link_BETA1-4 : bond 0.00663 ( 10) link_BETA1-4 : angle 2.31614 ( 30) link_ALPHA1-3 : bond 0.01842 ( 2) link_ALPHA1-3 : angle 2.02737 ( 6) hydrogen bonds : bond 0.03643 ( 559) hydrogen bonds : angle 4.42572 ( 1648) metal coordination : bond 0.00086 ( 4) covalent geometry : bond 0.00281 (13701) covalent geometry : angle 0.59596 (18580) *********************** 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 177 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 1.355 Fit side-chains REVERT: A 68 GLU cc_start: 0.8016 (tp30) cc_final: 0.7728 (mp0) REVERT: A 181 ARG cc_start: 0.8507 (mtm180) cc_final: 0.8290 (mtm180) REVERT: A 276 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8035 (mm-30) REVERT: A 285 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: A 495 GLU cc_start: 0.8800 (pp20) cc_final: 0.8588 (pp20) REVERT: A 537 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.8083 (t80) REVERT: A 563 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8627 (tm-30) REVERT: A 616 MET cc_start: 0.9161 (tpp) cc_final: 0.8816 (tpp) REVERT: A 623 LYS cc_start: 0.9167 (ttpp) cc_final: 0.8631 (pttm) REVERT: A 648 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8270 (mt-10) REVERT: A 651 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7795 (mp10) REVERT: A 653 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7152 (p90) REVERT: A 663 MET cc_start: 0.7790 (mtp) cc_final: 0.7451 (mtm) REVERT: E 63 ASP cc_start: 0.8717 (t70) cc_final: 0.8134 (m-30) REVERT: E 68 GLU cc_start: 0.8002 (tp30) cc_final: 0.7759 (mp0) REVERT: E 285 GLU cc_start: 0.8570 (tm-30) cc_final: 0.7853 (tm-30) REVERT: E 324 LYS cc_start: 0.9029 (ttmm) cc_final: 0.8823 (tmmt) REVERT: E 537 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7990 (t80) REVERT: E 616 MET cc_start: 0.9150 (tpp) cc_final: 0.8944 (tpp) REVERT: E 623 LYS cc_start: 0.9168 (ttpp) cc_final: 0.8610 (pttm) REVERT: E 651 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7935 (mp10) REVERT: E 653 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7194 (p90) REVERT: E 663 MET cc_start: 0.7749 (mtp) cc_final: 0.7381 (mtm) REVERT: H 95 TYR cc_start: 0.8516 (m-80) cc_final: 0.7824 (m-10) REVERT: Q 64 LYS cc_start: 0.8684 (ptmm) cc_final: 0.8346 (ptmt) REVERT: Q 95 TYR cc_start: 0.8318 (m-80) cc_final: 0.7888 (m-10) outliers start: 37 outliers final: 10 residues processed: 164 average time/residue: 1.1794 time to fit residues: 213.2502 Evaluate side-chains 149 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 651 GLN 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 537 TYR Chi-restraints excluded: chain E residue 651 GLN Chi-restraints excluded: chain E residue 653 PHE Chi-restraints excluded: chain H residue 22 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 114 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 92 optimal weight: 0.0060 chunk 31 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 150 optimal weight: 0.0010 chunk 48 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.9004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3554 r_free = 0.3554 target = 0.105849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.073153 restraints weight = 53370.449| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.76 r_work: 0.2809 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13725 Z= 0.123 Angle : 0.606 11.845 18640 Z= 0.296 Chirality : 0.043 0.160 2009 Planarity : 0.004 0.045 2390 Dihedral : 7.903 83.045 2383 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.52 % Allowed : 20.03 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1636 helix: 2.00 (0.22), residues: 521 sheet: -0.79 (0.28), residues: 286 loop : -0.41 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 36 HIS 0.004 0.001 HIS E 82 PHE 0.015 0.001 PHE E 506 TYR 0.014 0.001 TYR A 299 ARG 0.014 0.001 ARG E 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 6) link_NAG-ASN : angle 1.54127 ( 18) link_ALPHA1-6 : bond 0.00631 ( 2) link_ALPHA1-6 : angle 1.64730 ( 6) link_BETA1-4 : bond 0.00676 ( 10) link_BETA1-4 : angle 2.32309 ( 30) link_ALPHA1-3 : bond 0.01834 ( 2) link_ALPHA1-3 : angle 2.09238 ( 6) hydrogen bonds : bond 0.03505 ( 559) hydrogen bonds : angle 4.35281 ( 1648) metal coordination : bond 0.00080 ( 4) covalent geometry : bond 0.00282 (13701) covalent geometry : angle 0.59559 (18580) *********************** 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 179 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 1.482 Fit side-chains REVERT: A 68 GLU cc_start: 0.7973 (tp30) cc_final: 0.7692 (mp0) REVERT: A 276 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8106 (mm-30) REVERT: A 285 GLU cc_start: 0.8509 (tm-30) cc_final: 0.7755 (tm-30) REVERT: A 334 THR cc_start: 0.9048 (m) cc_final: 0.8705 (p) REVERT: A 489 GLU cc_start: 0.8457 (pm20) cc_final: 0.8146 (mp0) REVERT: A 495 GLU cc_start: 0.8788 (pp20) cc_final: 0.8580 (pp20) REVERT: A 537 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.8048 (t80) REVERT: A 563 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8634 (tm-30) REVERT: A 616 MET cc_start: 0.9163 (tpp) cc_final: 0.8903 (tpp) REVERT: A 623 LYS cc_start: 0.9177 (ttpp) cc_final: 0.8666 (pttm) REVERT: A 648 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8047 (tm-30) REVERT: A 651 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7806 (mp10) REVERT: A 653 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.6975 (p90) REVERT: A 663 MET cc_start: 0.7762 (mtp) cc_final: 0.7380 (mtm) REVERT: A 664 MET cc_start: 0.8507 (mmm) cc_final: 0.8213 (mtm) REVERT: E 63 ASP cc_start: 0.8743 (t70) cc_final: 0.8184 (m-30) REVERT: E 68 GLU cc_start: 0.7991 (tp30) cc_final: 0.7777 (mp0) REVERT: E 285 GLU cc_start: 0.8605 (tm-30) cc_final: 0.7891 (tm-30) REVERT: E 324 LYS cc_start: 0.9041 (ttmm) cc_final: 0.8806 (tmmt) REVERT: E 537 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7978 (t80) REVERT: E 623 LYS cc_start: 0.9189 (ttpp) cc_final: 0.8671 (pttm) REVERT: E 651 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: E 663 MET cc_start: 0.7712 (mtp) cc_final: 0.7360 (mtm) REVERT: H 3 GLN cc_start: 0.7622 (tp40) cc_final: 0.7245 (tp40) REVERT: H 82 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7874 (tp40) REVERT: H 95 TYR cc_start: 0.8531 (m-80) cc_final: 0.7755 (m-10) REVERT: Q 64 LYS cc_start: 0.8700 (ptmm) cc_final: 0.8327 (ptmt) REVERT: Q 95 TYR cc_start: 0.8337 (m-80) cc_final: 0.7917 (m-10) outliers start: 35 outliers final: 14 residues processed: 166 average time/residue: 1.1636 time to fit residues: 212.6048 Evaluate side-chains 157 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 289 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 651 GLN 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 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 31 THR Chi-restraints excluded: chain Q residue 69 THR 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 74 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 41 optimal weight: 0.0270 chunk 63 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3556 r_free = 0.3556 target = 0.106103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.073063 restraints weight = 71216.773| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 4.16 r_work: 0.2798 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13725 Z= 0.120 Angle : 0.608 11.302 18640 Z= 0.295 Chirality : 0.043 0.158 2009 Planarity : 0.004 0.052 2390 Dihedral : 7.679 82.311 2383 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.02 % Allowed : 20.53 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1636 helix: 2.03 (0.22), residues: 521 sheet: -0.77 (0.28), residues: 286 loop : -0.42 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 36 HIS 0.003 0.001 HIS E 82 PHE 0.011 0.001 PHE E 546 TYR 0.013 0.001 TYR A 299 ARG 0.013 0.001 ARG E 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 6) link_NAG-ASN : angle 1.48698 ( 18) link_ALPHA1-6 : bond 0.00593 ( 2) link_ALPHA1-6 : angle 1.64514 ( 6) link_BETA1-4 : bond 0.00675 ( 10) link_BETA1-4 : angle 2.29634 ( 30) link_ALPHA1-3 : bond 0.01964 ( 2) link_ALPHA1-3 : angle 2.23592 ( 6) hydrogen bonds : bond 0.03452 ( 559) hydrogen bonds : angle 4.31244 ( 1648) metal coordination : bond 0.00073 ( 4) covalent geometry : bond 0.00276 (13701) covalent geometry : angle 0.59815 (18580) *********************** 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 168 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.391 Fit side-chains REVERT: A 68 GLU cc_start: 0.7989 (tp30) cc_final: 0.7735 (mp0) REVERT: A 169 MET cc_start: 0.6672 (mmt) cc_final: 0.6451 (mmt) REVERT: A 276 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8166 (mm-30) REVERT: A 285 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: A 334 THR cc_start: 0.9048 (m) cc_final: 0.8724 (p) REVERT: A 489 GLU cc_start: 0.8455 (pm20) cc_final: 0.8185 (mp0) REVERT: A 495 GLU cc_start: 0.8786 (pp20) cc_final: 0.8568 (pp20) REVERT: A 537 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8044 (t80) REVERT: A 563 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8627 (tm-30) REVERT: A 616 MET cc_start: 0.9150 (tpp) cc_final: 0.8879 (tpp) REVERT: A 623 LYS cc_start: 0.9191 (ttpp) cc_final: 0.8703 (pttm) REVERT: A 648 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8078 (tm-30) REVERT: A 651 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: A 653 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6960 (p90) REVERT: A 663 MET cc_start: 0.7799 (mtp) cc_final: 0.7423 (mtm) REVERT: E 63 ASP cc_start: 0.8754 (t70) cc_final: 0.8225 (m-30) REVERT: E 68 GLU cc_start: 0.8018 (tp30) cc_final: 0.7801 (mp0) REVERT: E 109 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8533 (mm-30) REVERT: E 285 GLU cc_start: 0.8648 (tm-30) cc_final: 0.7925 (tm-30) REVERT: E 324 LYS cc_start: 0.9041 (ttmm) cc_final: 0.8796 (tmmt) REVERT: E 537 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7978 (t80) REVERT: E 563 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8691 (tm-30) REVERT: E 623 LYS cc_start: 0.9206 (ttpp) cc_final: 0.8708 (pttm) REVERT: E 651 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: E 663 MET cc_start: 0.7735 (mtp) cc_final: 0.7383 (mtm) REVERT: E 703 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8517 (mm-30) REVERT: H 82 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8021 (tp40) REVERT: H 95 TYR cc_start: 0.8554 (m-80) cc_final: 0.7795 (m-10) REVERT: Q 64 LYS cc_start: 0.8700 (ptmm) cc_final: 0.8310 (ptmt) REVERT: Q 95 TYR cc_start: 0.8389 (m-80) cc_final: 0.7819 (m-10) outliers start: 28 outliers final: 13 residues processed: 158 average time/residue: 1.1711 time to fit residues: 203.9489 Evaluate side-chains 155 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 651 GLN 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 100 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3530 r_free = 0.3530 target = 0.104319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.071234 restraints weight = 66534.526| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 4.04 r_work: 0.2767 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13725 Z= 0.168 Angle : 0.645 12.831 18640 Z= 0.314 Chirality : 0.044 0.169 2009 Planarity : 0.004 0.046 2390 Dihedral : 7.631 82.527 2383 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.38 % Allowed : 20.61 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1636 helix: 1.90 (0.22), residues: 523 sheet: -0.83 (0.28), residues: 286 loop : -0.45 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 36 HIS 0.004 0.001 HIS E 377 PHE 0.014 0.001 PHE E 506 TYR 0.017 0.001 TYR A 299 ARG 0.012 0.001 ARG E 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 6) link_NAG-ASN : angle 1.56414 ( 18) link_ALPHA1-6 : bond 0.00544 ( 2) link_ALPHA1-6 : angle 1.72036 ( 6) link_BETA1-4 : bond 0.00658 ( 10) link_BETA1-4 : angle 2.35083 ( 30) link_ALPHA1-3 : bond 0.01854 ( 2) link_ALPHA1-3 : angle 2.22339 ( 6) hydrogen bonds : bond 0.03808 ( 559) hydrogen bonds : angle 4.39897 ( 1648) metal coordination : bond 0.00181 ( 4) covalent geometry : bond 0.00396 (13701) covalent geometry : angle 0.63501 (18580) *********************** 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 170 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.392 Fit side-chains REVERT: A 68 GLU cc_start: 0.8002 (tp30) cc_final: 0.7740 (mp0) REVERT: A 276 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8151 (mm-30) REVERT: A 285 GLU cc_start: 0.8588 (tm-30) cc_final: 0.7842 (tm-30) REVERT: A 324 LYS cc_start: 0.8786 (tptp) cc_final: 0.8552 (tptp) REVERT: A 334 THR cc_start: 0.9081 (m) cc_final: 0.8776 (p) REVERT: A 489 GLU cc_start: 0.8495 (pm20) cc_final: 0.8191 (mp0) REVERT: A 495 GLU cc_start: 0.8791 (pp20) cc_final: 0.8563 (pp20) REVERT: A 537 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8058 (t80) REVERT: A 616 MET cc_start: 0.9214 (tpp) cc_final: 0.8938 (tpp) REVERT: A 623 LYS cc_start: 0.9217 (ttpp) cc_final: 0.8741 (pttm) REVERT: A 651 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: A 653 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.6980 (p90) REVERT: A 663 MET cc_start: 0.7816 (mtp) cc_final: 0.7419 (mtm) REVERT: E 63 ASP cc_start: 0.8766 (t70) cc_final: 0.8240 (m-30) REVERT: E 68 GLU cc_start: 0.8034 (tp30) cc_final: 0.7814 (mp0) REVERT: E 109 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8534 (mm-30) REVERT: E 285 GLU cc_start: 0.8656 (tm-30) cc_final: 0.7932 (tm-30) REVERT: E 324 LYS cc_start: 0.9068 (ttmm) cc_final: 0.8822 (tmmt) REVERT: E 537 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8105 (t80) REVERT: E 651 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: E 663 MET cc_start: 0.7772 (mtp) cc_final: 0.7398 (mtm) REVERT: H 95 TYR cc_start: 0.8560 (m-80) cc_final: 0.7787 (m-10) REVERT: Q 95 TYR cc_start: 0.8391 (m-80) cc_final: 0.7791 (m-10) outliers start: 33 outliers final: 13 residues processed: 159 average time/residue: 1.1950 time to fit residues: 209.6591 Evaluate side-chains 155 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 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 631 SER Chi-restraints excluded: chain A residue 651 GLN 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 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 Q residue 31 THR Chi-restraints excluded: chain Q residue 69 THR 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 71 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 160 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 139 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3555 r_free = 0.3555 target = 0.105759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.073164 restraints weight = 54287.427| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.76 r_work: 0.2816 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.5820 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= 0.124 Angle : 0.624 11.983 18640 Z= 0.302 Chirality : 0.043 0.193 2009 Planarity : 0.004 0.051 2390 Dihedral : 7.402 80.365 2383 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.73 % Allowed : 21.25 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1636 helix: 1.96 (0.22), residues: 523 sheet: -0.76 (0.28), residues: 286 loop : -0.45 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 36 HIS 0.004 0.001 HIS E 82 PHE 0.012 0.001 PHE E 546 TYR 0.030 0.001 TYR E 700 ARG 0.014 0.001 ARG E 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 6) link_NAG-ASN : angle 1.50696 ( 18) link_ALPHA1-6 : bond 0.00576 ( 2) link_ALPHA1-6 : angle 1.65635 ( 6) link_BETA1-4 : bond 0.00661 ( 10) link_BETA1-4 : angle 2.31694 ( 30) link_ALPHA1-3 : bond 0.01900 ( 2) link_ALPHA1-3 : angle 2.33980 ( 6) hydrogen bonds : bond 0.03510 ( 559) hydrogen bonds : angle 4.33246 ( 1648) metal coordination : bond 0.00090 ( 4) covalent geometry : bond 0.00290 (13701) covalent geometry : angle 0.61382 (18580) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.348 Fit side-chains REVERT: A 63 ASP cc_start: 0.8535 (t0) cc_final: 0.8063 (m-30) REVERT: A 68 GLU cc_start: 0.8000 (tp30) cc_final: 0.7763 (mp0) REVERT: A 169 MET cc_start: 0.6746 (mmt) cc_final: 0.6508 (mmt) REVERT: A 285 GLU cc_start: 0.8627 (tm-30) cc_final: 0.7871 (tm-30) REVERT: A 334 THR cc_start: 0.9092 (m) cc_final: 0.8799 (p) REVERT: A 489 GLU cc_start: 0.8465 (pm20) cc_final: 0.8165 (mp0) REVERT: A 495 GLU cc_start: 0.8770 (pp20) cc_final: 0.8555 (pp20) REVERT: A 537 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.8040 (t80) REVERT: A 563 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8634 (tm-30) REVERT: A 616 MET cc_start: 0.9173 (tpp) cc_final: 0.8929 (tpp) REVERT: A 623 LYS cc_start: 0.9197 (ttpp) cc_final: 0.8717 (pttm) REVERT: A 648 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8082 (tm-30) REVERT: A 651 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: A 653 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6884 (p90) REVERT: A 663 MET cc_start: 0.7753 (mtp) cc_final: 0.7366 (mtm) REVERT: A 704 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8263 (m) REVERT: E 63 ASP cc_start: 0.8734 (t70) cc_final: 0.8211 (m-30) REVERT: E 109 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8496 (mm-30) REVERT: E 285 GLU cc_start: 0.8667 (tm-30) cc_final: 0.7962 (tm-30) REVERT: E 324 LYS cc_start: 0.9050 (ttmm) cc_final: 0.8802 (tmmt) REVERT: E 537 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8144 (t80) REVERT: E 563 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8682 (tm-30) REVERT: E 651 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8035 (mp10) REVERT: E 663 MET cc_start: 0.7737 (mtp) cc_final: 0.7370 (mtm) REVERT: H 95 TYR cc_start: 0.8572 (m-80) cc_final: 0.7689 (m-10) REVERT: Q 95 TYR cc_start: 0.8433 (m-80) cc_final: 0.7782 (m-10) outliers start: 24 outliers final: 10 residues processed: 152 average time/residue: 1.2408 time to fit residues: 206.8650 Evaluate side-chains 148 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL 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 537 TYR Chi-restraints excluded: chain A residue 651 GLN Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain 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 31 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3559 r_free = 0.3559 target = 0.105995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.073427 restraints weight = 65754.616| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.99 r_work: 0.2809 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.5863 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= 0.127 Angle : 0.648 12.330 18640 Z= 0.312 Chirality : 0.043 0.199 2009 Planarity : 0.004 0.052 2390 Dihedral : 7.218 79.518 2383 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.30 % Allowed : 21.61 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1636 helix: 1.97 (0.22), residues: 523 sheet: -0.73 (0.28), residues: 286 loop : -0.45 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 36 HIS 0.003 0.001 HIS E 82 PHE 0.014 0.001 PHE E 506 TYR 0.018 0.001 TYR E 700 ARG 0.014 0.001 ARG E 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 6) link_NAG-ASN : angle 1.49592 ( 18) link_ALPHA1-6 : bond 0.00558 ( 2) link_ALPHA1-6 : angle 1.68677 ( 6) link_BETA1-4 : bond 0.00661 ( 10) link_BETA1-4 : angle 2.32414 ( 30) link_ALPHA1-3 : bond 0.01891 ( 2) link_ALPHA1-3 : angle 2.38812 ( 6) hydrogen bonds : bond 0.03487 ( 559) hydrogen bonds : angle 4.31193 ( 1648) metal coordination : bond 0.00086 ( 4) covalent geometry : bond 0.00299 (13701) covalent geometry : angle 0.63852 (18580) ********************** 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 155 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 1.498 Fit side-chains REVERT: A 63 ASP cc_start: 0.8504 (t0) cc_final: 0.8043 (m-30) REVERT: A 68 GLU cc_start: 0.8011 (tp30) cc_final: 0.7775 (mp0) REVERT: A 169 MET cc_start: 0.6705 (mmt) cc_final: 0.6447 (mmt) REVERT: A 285 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: A 324 LYS cc_start: 0.8716 (tptp) cc_final: 0.8383 (ttmm) REVERT: A 334 THR cc_start: 0.9092 (m) cc_final: 0.8791 (p) REVERT: A 489 GLU cc_start: 0.8500 (pm20) cc_final: 0.8173 (mp0) REVERT: A 495 GLU cc_start: 0.8762 (pp20) cc_final: 0.8549 (pp20) REVERT: A 537 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.8068 (t80) REVERT: A 563 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8645 (tm-30) REVERT: A 616 MET cc_start: 0.9210 (tpp) cc_final: 0.8951 (tpp) REVERT: A 648 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8100 (tm-30) REVERT: A 651 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: A 663 MET cc_start: 0.7719 (mtp) cc_final: 0.7297 (mtm) REVERT: A 704 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8262 (m) REVERT: E 63 ASP cc_start: 0.8731 (t70) cc_final: 0.8210 (m-30) REVERT: E 109 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8528 (mm-30) REVERT: E 285 GLU cc_start: 0.8685 (tm-30) cc_final: 0.7973 (tm-30) REVERT: E 324 LYS cc_start: 0.9099 (ttmm) cc_final: 0.8841 (tmmt) REVERT: E 537 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8133 (t80) REVERT: E 651 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8079 (mp10) REVERT: E 663 MET cc_start: 0.7745 (mtp) cc_final: 0.7379 (mtm) REVERT: H 95 TYR cc_start: 0.8562 (m-80) cc_final: 0.7665 (m-10) REVERT: Q 95 TYR cc_start: 0.8457 (m-80) cc_final: 0.7785 (m-10) REVERT: Q 100 ARG cc_start: 0.8742 (mmm160) cc_final: 0.8527 (mmm160) outliers start: 18 outliers final: 10 residues processed: 145 average time/residue: 1.2269 time to fit residues: 195.5472 Evaluate side-chains 152 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 325 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 651 GLN Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain 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 31 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 40 optimal weight: 3.9990 chunk 135 optimal weight: 0.0570 chunk 142 optimal weight: 0.2980 chunk 112 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 62 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.107537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.074943 restraints weight = 67331.207| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.08 r_work: 0.2842 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.5967 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= 0.110 Angle : 0.626 12.247 18640 Z= 0.300 Chirality : 0.042 0.164 2009 Planarity : 0.004 0.050 2390 Dihedral : 6.881 77.228 2383 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.15 % Allowed : 22.05 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1636 helix: 2.14 (0.22), residues: 519 sheet: -0.69 (0.28), residues: 286 loop : -0.36 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 36 HIS 0.004 0.001 HIS E 82 PHE 0.011 0.001 PHE E 546 TYR 0.016 0.001 TYR E 700 ARG 0.015 0.001 ARG E 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 6) link_NAG-ASN : angle 1.45345 ( 18) link_ALPHA1-6 : bond 0.00553 ( 2) link_ALPHA1-6 : angle 1.65146 ( 6) link_BETA1-4 : bond 0.00679 ( 10) link_BETA1-4 : angle 2.28714 ( 30) link_ALPHA1-3 : bond 0.01899 ( 2) link_ALPHA1-3 : angle 2.48170 ( 6) hydrogen bonds : bond 0.03247 ( 559) hydrogen bonds : angle 4.21519 ( 1648) metal coordination : bond 0.00026 ( 4) covalent geometry : bond 0.00256 (13701) covalent geometry : angle 0.61589 (18580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10982.46 seconds wall clock time: 187 minutes 36.37 seconds (11256.37 seconds total)