Starting phenix.real_space_refine on Fri Jul 3 16:55:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvl_52437/07_2026/9hvl_52437.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvl_52437/07_2026/9hvl_52437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hvl_52437/07_2026/9hvl_52437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvl_52437/07_2026/9hvl_52437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hvl_52437/07_2026/9hvl_52437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvl_52437/07_2026/9hvl_52437.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1790 atoms to isotropic. 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 8443 2.51 5 N 2185 2.21 5 O 2567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13246 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: 5544 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: 5686 Chain: "H" Number of atoms: 895 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 115, 892 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 115, 892 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain breaks: 1 bond proxies already assigned to first conformer: 906 Chain: "P" Number of atoms: 895 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 115, 892 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 115, 892 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain breaks: 1 bond proxies already assigned to first conformer: 906 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 58 Ad-hoc single atom residues: {' CA': 1, ' CL': 1} Unusual residues: {' ZN': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AVAL E 660 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL E 660 " occ=0.50 Time building chain proxies: 4.26, per 1000 atoms: 0.32 Number of scatterers: 13246 At special positions: 0 Unit cell: (155.75, 86.33, 96.12, 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 2567 8.00 N 2185 7.00 C 8443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A 801 " - " ASN A 121 " " NAG A 802 " - " ASN A 140 " " NAG A 804 " - " ASN A 459 " " NAG E 801 " - " ASN E 121 " " NAG E 802 " - " ASN E 140 " " NAG E 804 " - " ASN E 459 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 798.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" NE2 HIS A 553 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" NE2 HIS A 377 " pdb=" ZN E 805 " pdb="ZN ZN E 805 " - pdb=" NE2 HIS E 553 " pdb=" ZN E 806 " pdb="ZN ZN E 806 " - pdb=" NE2 HIS E 377 " 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2982 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 13 sheets defined 37.4% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 66 through 78 Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.546A pdb=" N GLY A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.978A pdb=" N LEU A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 301 through 308 removed outlier: 4.349A pdb=" N LYS A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 388 through 408 removed outlier: 3.816A pdb=" N VAL A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 408 " --> pdb=" O THR A 404 " (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: 4.329A pdb=" N GLU A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.509A pdb=" N SER A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 527 removed outlier: 3.647A pdb=" N ARG A 527 " --> pdb=" O VAL A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 566 removed outlier: 3.693A pdb=" N VAL A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 589 removed outlier: 3.693A pdb=" N VAL A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 617 removed outlier: 4.222A pdb=" N TYR A 600 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 629 through 650 Processing helix chain 'A' and resid 657 through 675 removed outlier: 4.147A pdb=" N GLU A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG A 673 " --> pdb=" O MET A 669 " (cutoff:3.500A) removed outlier: 3.882A 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 removed outlier: 3.548A pdb=" N LYS A 718 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 745 Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 66 through 78 Processing helix chain 'E' and resid 86 through 104 removed outlier: 3.538A pdb=" N GLY E 104 " --> pdb=" O TRP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 191 removed outlier: 3.871A pdb=" N LEU E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU E 189 " --> pdb=" O PHE E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 241 through 245 Processing helix chain 'E' and resid 301 through 308 removed outlier: 4.346A pdb=" N LYS E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 388 through 408 removed outlier: 3.708A pdb=" N VAL E 394 " --> pdb=" O SER E 390 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) 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: 4.412A pdb=" N GLU E 444 " --> pdb=" O ARG E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 480 Processing helix chain 'E' and resid 492 through 501 removed outlier: 3.536A pdb=" N SER E 496 " --> pdb=" O SER E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 527 removed outlier: 3.648A pdb=" N ARG E 527 " --> pdb=" O VAL E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 566 removed outlier: 3.715A pdb=" N VAL E 562 " --> pdb=" O THR E 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 586 removed outlier: 3.617A pdb=" N VAL E 576 " --> pdb=" O TYR E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 616 removed outlier: 4.229A pdb=" N TYR E 600 " --> pdb=" O ASP E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 625 Processing helix chain 'E' and resid 629 through 650 Processing helix chain 'E' and resid 657 through 675 removed outlier: 4.178A pdb=" N GLU E 672 " --> pdb=" O LEU E 668 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG E 673 " --> pdb=" O MET E 669 " (cutoff:3.500A) removed outlier: 3.883A 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: 3.556A 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 'P' and resid 61 through 65 Processing helix chain 'P' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 119 removed outlier: 3.541A pdb=" N SER A 107 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 9.643A pdb=" N GLY A 446 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N ASP A 369 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N ALA A 448 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR A 371 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE A 450 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE A 373 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 172 removed outlier: 3.546A pdb=" N PHE A 139 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA H 98 " --> pdb=" O TYR H 113 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR H 113 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 removed outlier: 3.546A pdb=" N PHE A 139 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 163 removed outlier: 7.328A pdb=" N GLY A 256 " --> pdb=" O ALA A 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 178 removed outlier: 6.508A pdb=" N ARG A 204 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 225 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ILE A 297 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 227 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 513 removed outlier: 8.551A pdb=" N SER A 513 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 464 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 461 " --> pdb=" O THR A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 107 through 119 removed outlier: 9.496A pdb=" N GLY E 446 " --> pdb=" O GLU E 367 " (cutoff:3.500A) removed outlier: 11.077A pdb=" N ASP E 369 " --> pdb=" O GLY E 446 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N ALA E 448 " --> pdb=" O ASP E 369 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR E 371 " --> pdb=" O ALA E 448 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE E 450 " --> pdb=" O TYR E 371 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE E 373 " --> pdb=" O ILE E 450 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 171 through 172 removed outlier: 3.545A pdb=" N PHE E 139 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N MET P 34 " --> pdb=" O GLY P 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 162 through 163 removed outlier: 7.324A pdb=" N GLY E 256 " --> pdb=" O ALA E 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 174 through 178 removed outlier: 6.511A pdb=" N ARG E 204 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL E 225 " --> pdb=" O HIS E 295 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE E 297 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU E 227 " --> pdb=" O ILE E 297 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 512 through 513 removed outlier: 8.601A pdb=" N SER E 513 " --> pdb=" O LEU E 462 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL E 464 " --> pdb=" O SER E 513 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR E 461 " --> pdb=" O THR E 538 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'P' and resid 3 through 7 561 hydrogen bonds defined for protein. 1534 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: 1.99 Time building geometry restraints manager: 1.53 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: 4197 1.34 - 1.46: 3317 1.46 - 1.58: 5999 1.58 - 1.70: 1 1.70 - 1.82: 78 Bond restraints: 13592 Sorted by residual: bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.587 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.568 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" C5 MAN I 4 " pdb=" O5 MAN I 4 " ideal model delta sigma weight residual 1.418 1.459 -0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" C1 MAN I 4 " pdb=" O5 MAN I 4 " ideal model delta sigma weight residual 1.399 1.437 -0.038 2.00e-02 2.50e+03 3.70e+00 ... (remaining 13587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 18123 2.29 - 4.58: 259 4.58 - 6.87: 45 6.87 - 9.17: 1 9.17 - 11.46: 1 Bond angle restraints: 18429 Sorted by residual: angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 113.20 108.35 4.85 9.60e-01 1.09e+00 2.55e+01 angle pdb=" N VAL E 177 " pdb=" CA VAL E 177 " pdb=" C VAL E 177 " ideal model delta sigma weight residual 113.20 108.44 4.76 9.60e-01 1.09e+00 2.46e+01 angle pdb=" N LEU A 587 " pdb=" CA LEU A 587 " pdb=" C LEU A 587 " ideal model delta sigma weight residual 114.64 108.31 6.33 1.52e+00 4.33e-01 1.74e+01 angle pdb=" CB MET E 569 " pdb=" CG MET E 569 " pdb=" SD MET E 569 " ideal model delta sigma weight residual 112.70 124.16 -11.46 3.00e+00 1.11e-01 1.46e+01 angle pdb=" N LEU E 587 " pdb=" CA LEU E 587 " pdb=" C LEU E 587 " ideal model delta sigma weight residual 114.64 108.85 5.79 1.52e+00 4.33e-01 1.45e+01 ... (remaining 18424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.03: 7604 23.03 - 46.07: 605 46.07 - 69.10: 135 69.10 - 92.14: 41 92.14 - 115.17: 24 Dihedral angle restraints: 8409 sinusoidal: 3715 harmonic: 4694 Sorted by residual: dihedral pdb=" CA VAL A 399 " pdb=" C VAL A 399 " pdb=" N ARG A 400 " pdb=" CA ARG A 400 " ideal model delta harmonic sigma weight residual 180.00 141.41 38.59 0 5.00e+00 4.00e-02 5.96e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.22 41.78 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CA ILE E 283 " pdb=" C ILE E 283 " pdb=" N ALA E 284 " pdb=" CA ALA E 284 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 8406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1675 0.059 - 0.118: 293 0.118 - 0.176: 20 0.176 - 0.235: 3 0.235 - 0.294: 3 Chirality restraints: 1994 Sorted by residual: chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.16e+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 -2.55 0.28 2.00e-01 2.50e+01 1.92e+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 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 1991 not shown) Planarity restraints: 2372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 314 " -0.060 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO E 315 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO E 315 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 315 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 300 " 0.022 2.00e-02 2.50e+03 1.66e-02 5.53e+00 pdb=" CG TYR A 300 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 300 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 300 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 300 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 300 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 300 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 300 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 387 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO E 388 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 388 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 388 " -0.024 5.00e-02 4.00e+02 ... (remaining 2369 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 166 2.59 - 3.17: 10823 3.17 - 3.75: 21512 3.75 - 4.32: 31835 4.32 - 4.90: 51270 Nonbonded interactions: 115606 Sorted by model distance: nonbonded pdb=" OD2 ASP E 387 " pdb="ZN ZN E 805 " model vdw 2.017 2.230 nonbonded pdb=" OD2 ASP A 387 " pdb="ZN ZN A 805 " model vdw 2.018 2.230 nonbonded pdb=" OD1 ASP A 387 " pdb="ZN ZN A 806 " model vdw 2.072 2.230 nonbonded pdb=" OD1 ASP E 387 " pdb="ZN ZN E 806 " model vdw 2.073 2.230 nonbonded pdb=" OE1 GLU E 425 " pdb="ZN ZN E 805 " model vdw 2.129 2.230 ... (remaining 115601 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 659 or resid 661 through 807)) selection = (chain 'E' and (resid 56 through 659 or resid 661 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 2 through 102 or resid 104 through 122)) selection = (chain 'P' and (resid 2 through 102 or resid 104 through 122)) } 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.170 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 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 0.068 13618 Z= 0.171 Angle : 0.669 11.458 18493 Z= 0.343 Chirality : 0.046 0.294 1994 Planarity : 0.005 0.090 2366 Dihedral : 18.638 115.171 5421 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.20 % Allowed : 21.21 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.21), residues: 1613 helix: 0.30 (0.22), residues: 511 sheet: -0.66 (0.30), residues: 296 loop : -0.59 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 730 TYR 0.039 0.001 TYR A 300 PHE 0.009 0.001 PHE P 37 TRP 0.010 0.001 TRP E 421 HIS 0.005 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (13592) covalent geometry : angle 0.65520 / 0.34 (18429) SS BOND : bond 0.00078 / 0.04 ( 2) SS BOND : angle 0.96226 / 0.55 ( 4) hydrogen bonds : bond 0.15252 / 9.50 ( 537) hydrogen bonds : angle 7.02186 / 4.99 ( 1534) metal coordination : bond 0.00177 / 0.09 ( 4) link_ALPHA1-3 : bond 0.00832 / 0.40 ( 2) link_ALPHA1-3 : angle 2.18289 / 1.72 ( 6) link_ALPHA1-6 : bond 0.00679 / 0.34 ( 2) link_ALPHA1-6 : angle 1.98594 / 1.74 ( 6) link_BETA1-4 : bond 0.00834 / 0.57 ( 10) link_BETA1-4 : angle 2.83754 / 2.10 ( 30) link_NAG-ASN : bond 0.00544 / 0.30 ( 6) link_NAG-ASN : angle 1.93985 / 1.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.6634 (mtp) cc_final: 0.6404 (mpp) REVERT: E 192 MET cc_start: 0.6016 (mpt) cc_final: 0.5507 (mmp) REVERT: E 598 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7317 (mtm180) outliers start: 44 outliers final: 40 residues processed: 177 average time/residue: 0.4644 time to fit residues: 91.5489 Evaluate side-chains 172 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 600 TYR Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 530 ILE Chi-restraints excluded: chain E residue 590 SER Chi-restraints excluded: chain E residue 631 SER Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 105 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS A 136 ASN A 153 ASN E 56 HIS E 153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.171782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.129453 restraints weight = 29165.303| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 4.14 r_work: 0.3163 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13618 Z= 0.193 Angle : 0.697 15.869 18493 Z= 0.349 Chirality : 0.048 0.247 1994 Planarity : 0.005 0.059 2366 Dihedral : 13.696 108.550 2417 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.72 % Allowed : 19.10 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.21), residues: 1613 helix: 0.09 (0.21), residues: 531 sheet: -0.61 (0.29), residues: 290 loop : -0.77 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 99 TYR 0.032 0.002 TYR A 300 PHE 0.012 0.002 PHE A 737 TRP 0.012 0.002 TRP A 421 HIS 0.006 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (13592) covalent geometry : angle 0.66445 / 0.34 (18429) SS BOND : bond 0.00128 / 0.06 ( 2) SS BOND : angle 0.78270 / 0.46 ( 4) hydrogen bonds : bond 0.04402 / 2.87 ( 537) hydrogen bonds : angle 5.59972 / 4.05 ( 1534) metal coordination : bond 0.00543 / 0.27 ( 4) link_ALPHA1-3 : bond 0.01178 / 0.58 ( 2) link_ALPHA1-3 : angle 2.79474 / 1.88 ( 6) link_ALPHA1-6 : bond 0.00610 / 0.32 ( 2) link_ALPHA1-6 : angle 2.77056 / 2.39 ( 6) link_BETA1-4 : bond 0.01059 / 0.78 ( 10) link_BETA1-4 : angle 2.92316 / 2.15 ( 30) link_NAG-ASN : bond 0.00869 / 0.48 ( 6) link_NAG-ASN : angle 5.23156 / 3.79 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 138 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 425 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: A 730 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7753 (ttp-110) REVERT: E 68 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5660 (tp30) REVERT: E 425 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7194 (mm-30) REVERT: E 569 MET cc_start: 0.6855 (mmm) cc_final: 0.6641 (mmm) outliers start: 65 outliers final: 28 residues processed: 183 average time/residue: 0.5596 time to fit residues: 111.9857 Evaluate side-chains 162 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 554 SER Chi-restraints excluded: chain E residue 631 SER Chi-restraints excluded: chain E residue 667 GLN Chi-restraints excluded: chain E residue 714 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 152 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 94 optimal weight: 0.0970 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS A 153 ASN A 589 ASN A 620 GLN E 56 HIS E 153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.173929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124379 restraints weight = 33595.818| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.12 r_work: 0.3221 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13618 Z= 0.132 Angle : 0.617 12.801 18493 Z= 0.308 Chirality : 0.045 0.261 1994 Planarity : 0.004 0.049 2366 Dihedral : 11.260 102.051 2389 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.07 % Allowed : 19.24 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.21), residues: 1613 helix: 0.47 (0.22), residues: 531 sheet: -0.38 (0.30), residues: 284 loop : -0.73 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 255 TYR 0.029 0.001 TYR E 277 PHE 0.018 0.001 PHE A 653 TRP 0.010 0.001 TRP E 421 HIS 0.004 0.001 HIS E 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13592) covalent geometry : angle 0.59051 / 0.30 (18429) SS BOND : bond 0.00093 / 0.05 ( 2) SS BOND : angle 0.48951 / 0.31 ( 4) hydrogen bonds : bond 0.03598 / 2.33 ( 537) hydrogen bonds : angle 5.18914 / 3.77 ( 1534) metal coordination : bond 0.00306 / 0.15 ( 4) link_ALPHA1-3 : bond 0.01487 / 0.74 ( 2) link_ALPHA1-3 : angle 2.46684 / 1.83 ( 6) link_ALPHA1-6 : bond 0.01171 / 0.61 ( 2) link_ALPHA1-6 : angle 2.40282 / 1.87 ( 6) link_BETA1-4 : bond 0.00906 / 0.68 ( 10) link_BETA1-4 : angle 2.60628 / 1.84 ( 30) link_NAG-ASN : bond 0.00425 / 0.25 ( 6) link_NAG-ASN : angle 4.32981 / 3.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 0.533 Fit side-chains REVERT: A 68 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.5665 (tp30) REVERT: A 169 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.5975 (mpt) REVERT: A 511 ARG cc_start: 0.7331 (tmm-80) cc_final: 0.7129 (ttt90) REVERT: A 730 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7665 (ttp-110) REVERT: E 68 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.5674 (tp30) REVERT: E 425 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7008 (mm-30) REVERT: E 653 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.6292 (t80) REVERT: E 716 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: E 723 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7429 (mtpp) REVERT: E 730 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7766 (ttp-110) outliers start: 56 outliers final: 21 residues processed: 176 average time/residue: 0.5933 time to fit residues: 114.2318 Evaluate side-chains 165 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 653 PHE Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 716 GLU Chi-restraints excluded: chain E residue 723 LYS Chi-restraints excluded: chain E residue 730 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 110 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS A 153 ASN E 56 HIS E 153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.175024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126565 restraints weight = 35280.314| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.41 r_work: 0.3244 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13618 Z= 0.111 Angle : 0.596 17.258 18493 Z= 0.295 Chirality : 0.044 0.223 1994 Planarity : 0.004 0.049 2366 Dihedral : 10.617 103.592 2383 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.21 % Allowed : 19.39 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.21), residues: 1613 helix: 0.71 (0.22), residues: 531 sheet: -0.33 (0.30), residues: 286 loop : -0.65 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 255 TYR 0.026 0.001 TYR E 277 PHE 0.012 0.001 PHE A 653 TRP 0.009 0.001 TRP E 421 HIS 0.004 0.001 HIS E 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (13592) covalent geometry : angle 0.56773 / 0.29 (18429) SS BOND : bond 0.00118 / 0.06 ( 2) SS BOND : angle 0.43964 / 0.28 ( 4) hydrogen bonds : bond 0.03255 / 2.10 ( 537) hydrogen bonds : angle 5.03212 / 3.66 ( 1534) metal coordination : bond 0.00159 / 0.08 ( 4) link_ALPHA1-3 : bond 0.01440 / 0.71 ( 2) link_ALPHA1-3 : angle 2.49188 / 1.78 ( 6) link_ALPHA1-6 : bond 0.00765 / 0.40 ( 2) link_ALPHA1-6 : angle 2.11703 / 1.75 ( 6) link_BETA1-4 : bond 0.00897 / 0.67 ( 10) link_BETA1-4 : angle 2.49504 / 1.78 ( 30) link_NAG-ASN : bond 0.00803 / 0.43 ( 6) link_NAG-ASN : angle 4.62500 / 4.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 141 time to evaluate : 0.503 Fit side-chains REVERT: A 68 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.5692 (tp30) REVERT: A 425 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: A 730 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7649 (ttp-110) REVERT: E 716 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7699 (mm-30) REVERT: E 723 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7451 (mtpp) REVERT: E 730 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7864 (ttp-110) outliers start: 58 outliers final: 30 residues processed: 185 average time/residue: 0.5809 time to fit residues: 118.0779 Evaluate side-chains 171 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 667 GLN Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 716 GLU Chi-restraints excluded: chain E residue 723 LYS Chi-restraints excluded: chain E residue 730 ARG Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain P residue 105 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 150 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS A 153 ASN E 56 HIS E 153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.168954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118817 restraints weight = 26540.938| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.80 r_work: 0.3165 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 13618 Z= 0.317 Angle : 0.803 17.623 18493 Z= 0.406 Chirality : 0.053 0.317 1994 Planarity : 0.006 0.070 2366 Dihedral : 10.822 102.612 2381 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 5.30 % Allowed : 18.66 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.20), residues: 1613 helix: -0.15 (0.21), residues: 521 sheet: -0.50 (0.30), residues: 284 loop : -0.90 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 511 TYR 0.033 0.003 TYR E 300 PHE 0.022 0.003 PHE E 570 TRP 0.016 0.002 TRP E 421 HIS 0.009 0.002 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.32 (13592) covalent geometry : angle 0.77925 / 0.40 (18429) SS BOND : bond 0.00178 / 0.09 ( 2) SS BOND : angle 0.83054 / 0.49 ( 4) hydrogen bonds : bond 0.04780 / 3.11 ( 537) hydrogen bonds : angle 5.57766 / 4.03 ( 1534) metal coordination : bond 0.00783 / 0.38 ( 4) link_ALPHA1-3 : bond 0.01396 / 0.68 ( 2) link_ALPHA1-3 : angle 2.67314 / 1.90 ( 6) link_ALPHA1-6 : bond 0.00586 / 0.31 ( 2) link_ALPHA1-6 : angle 2.66849 / 2.34 ( 6) link_BETA1-4 : bond 0.01078 / 0.86 ( 10) link_BETA1-4 : angle 2.89218 / 2.15 ( 30) link_NAG-ASN : bond 0.00663 / 0.37 ( 6) link_NAG-ASN : angle 4.76549 / 4.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 127 time to evaluate : 0.492 Fit side-chains REVERT: A 563 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: A 605 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7061 (ttt90) REVERT: A 716 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: A 730 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7942 (ttp-110) REVERT: E 653 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6269 (t80) REVERT: E 716 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: E 723 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7663 (mtpp) REVERT: E 730 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8017 (ttp-110) outliers start: 73 outliers final: 39 residues processed: 179 average time/residue: 0.5431 time to fit residues: 106.4016 Evaluate side-chains 172 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 322 SER 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 404 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 667 GLN Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 554 SER Chi-restraints excluded: chain E residue 653 PHE Chi-restraints excluded: chain E residue 667 GLN Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 716 GLU Chi-restraints excluded: chain E residue 723 LYS Chi-restraints excluded: chain E residue 730 ARG Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain P residue 105 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 119 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 14 optimal weight: 0.0670 chunk 82 optimal weight: 0.0050 chunk 56 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 overall best weight: 0.8334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS A 153 ASN E 56 HIS E 153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.173723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125882 restraints weight = 33783.796| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.39 r_work: 0.3234 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13618 Z= 0.122 Angle : 0.613 14.069 18493 Z= 0.307 Chirality : 0.045 0.235 1994 Planarity : 0.004 0.050 2366 Dihedral : 9.834 105.795 2379 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.85 % Allowed : 20.41 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.21), residues: 1613 helix: 0.50 (0.22), residues: 523 sheet: -0.41 (0.30), residues: 284 loop : -0.72 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 511 TYR 0.029 0.001 TYR E 277 PHE 0.013 0.001 PHE A 653 TRP 0.011 0.001 TRP E 421 HIS 0.005 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (13592) covalent geometry : angle 0.59114 / 0.30 (18429) SS BOND : bond 0.00106 / 0.05 ( 2) SS BOND : angle 0.32047 / 0.23 ( 4) hydrogen bonds : bond 0.03381 / 2.18 ( 537) hydrogen bonds : angle 5.08298 / 3.69 ( 1534) metal coordination : bond 0.00222 / 0.11 ( 4) link_ALPHA1-3 : bond 0.01516 / 0.75 ( 2) link_ALPHA1-3 : angle 2.55930 / 1.83 ( 6) link_ALPHA1-6 : bond 0.00566 / 0.29 ( 2) link_ALPHA1-6 : angle 2.10152 / 1.75 ( 6) link_BETA1-4 : bond 0.00968 / 0.76 ( 10) link_BETA1-4 : angle 2.21396 / 1.56 ( 30) link_NAG-ASN : bond 0.00414 / 0.26 ( 6) link_NAG-ASN : angle 4.00549 / 3.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 132 time to evaluate : 0.498 Fit side-chains REVERT: A 68 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5665 (tp30) REVERT: A 495 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7173 (tt0) REVERT: A 716 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: A 730 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7588 (ttp-110) REVERT: E 68 GLU cc_start: 0.5661 (mp0) cc_final: 0.5208 (tm-30) REVERT: E 289 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8418 (mp) REVERT: E 716 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: E 723 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7460 (mtpp) REVERT: E 730 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7842 (ttp-110) outliers start: 53 outliers final: 33 residues processed: 171 average time/residue: 0.5026 time to fit residues: 94.8398 Evaluate side-chains 166 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 554 SER Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 716 GLU Chi-restraints excluded: chain E residue 723 LYS Chi-restraints excluded: chain E residue 730 ARG Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain P residue 105 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 71 optimal weight: 0.0370 chunk 20 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 138 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS A 153 ASN E 56 HIS E 124 HIS E 153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.176010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127349 restraints weight = 29134.668| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.66 r_work: 0.3288 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13618 Z= 0.106 Angle : 0.572 10.716 18493 Z= 0.286 Chirality : 0.043 0.229 1994 Planarity : 0.004 0.050 2366 Dihedral : 8.979 105.697 2379 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.78 % Allowed : 20.70 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.21), residues: 1613 helix: 0.87 (0.22), residues: 531 sheet: -0.14 (0.30), residues: 284 loop : -0.59 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 511 TYR 0.026 0.001 TYR E 277 PHE 0.013 0.001 PHE A 653 TRP 0.011 0.001 TRP E 421 HIS 0.003 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (13592) covalent geometry : angle 0.55507 / 0.28 (18429) SS BOND : bond 0.00107 / 0.06 ( 2) SS BOND : angle 0.40385 / 0.24 ( 4) hydrogen bonds : bond 0.03039 / 1.95 ( 537) hydrogen bonds : angle 4.83934 / 3.52 ( 1534) metal coordination : bond 0.00181 / 0.09 ( 4) link_ALPHA1-3 : bond 0.01348 / 0.66 ( 2) link_ALPHA1-3 : angle 2.48619 / 1.72 ( 6) link_ALPHA1-6 : bond 0.00485 / 0.25 ( 2) link_ALPHA1-6 : angle 2.04684 / 1.70 ( 6) link_BETA1-4 : bond 0.00952 / 0.72 ( 10) link_BETA1-4 : angle 2.15493 / 1.56 ( 30) link_NAG-ASN : bond 0.00236 / 0.14 ( 6) link_NAG-ASN : angle 3.10762 / 2.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 0.433 Fit side-chains REVERT: A 68 GLU cc_start: 0.5850 (OUTLIER) cc_final: 0.5374 (tm-30) REVERT: A 716 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7781 (mm-30) REVERT: A 730 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7688 (ttp-110) REVERT: E 68 GLU cc_start: 0.5715 (OUTLIER) cc_final: 0.5181 (tm-30) REVERT: E 289 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8309 (mp) REVERT: E 511 ARG cc_start: 0.7451 (tmm-80) cc_final: 0.7247 (ttt90) REVERT: E 716 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7699 (mm-30) REVERT: E 723 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7399 (mtpp) REVERT: E 730 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7930 (ttp-110) outliers start: 52 outliers final: 31 residues processed: 180 average time/residue: 0.5338 time to fit residues: 106.2982 Evaluate side-chains 172 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 322 SER 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 405 LEU Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 618 HIS Chi-restraints excluded: chain E residue 667 GLN Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 716 GLU Chi-restraints excluded: chain E residue 723 LYS Chi-restraints excluded: chain E residue 730 ARG Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain P residue 105 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 27 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 218 GLN E 56 HIS E 124 HIS E 153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.171967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.123786 restraints weight = 31876.496| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.21 r_work: 0.3209 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13618 Z= 0.188 Angle : 0.681 14.273 18493 Z= 0.340 Chirality : 0.047 0.207 1994 Planarity : 0.005 0.046 2366 Dihedral : 9.016 102.955 2374 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.99 % Allowed : 20.84 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.21), residues: 1613 helix: 0.37 (0.21), residues: 537 sheet: -0.25 (0.30), residues: 284 loop : -0.68 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 511 TYR 0.029 0.002 TYR E 277 PHE 0.014 0.002 PHE E 570 TRP 0.013 0.002 TRP E 421 HIS 0.005 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (13592) covalent geometry : angle 0.64731 / 0.33 (18429) SS BOND : bond 0.00141 / 0.07 ( 2) SS BOND : angle 0.62561 / 0.37 ( 4) hydrogen bonds : bond 0.03770 / 2.44 ( 537) hydrogen bonds : angle 5.09238 / 3.69 ( 1534) metal coordination : bond 0.00495 / 0.24 ( 4) link_ALPHA1-3 : bond 0.01369 / 0.67 ( 2) link_ALPHA1-3 : angle 2.70630 / 1.84 ( 6) link_ALPHA1-6 : bond 0.00353 / 0.18 ( 2) link_ALPHA1-6 : angle 2.08733 / 1.79 ( 6) link_BETA1-4 : bond 0.00985 / 0.75 ( 10) link_BETA1-4 : angle 2.32477 / 1.71 ( 30) link_NAG-ASN : bond 0.00547 / 0.34 ( 6) link_NAG-ASN : angle 5.81235 / 4.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 128 time to evaluate : 0.556 Fit side-chains REVERT: A 68 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5622 (tp30) REVERT: A 716 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: A 730 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7783 (ttp-110) REVERT: E 716 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: E 723 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7432 (mtpp) REVERT: E 730 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7960 (ttp-110) outliers start: 55 outliers final: 34 residues processed: 167 average time/residue: 0.5454 time to fit residues: 100.2576 Evaluate side-chains 167 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 554 SER Chi-restraints excluded: chain E residue 667 GLN Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 716 GLU Chi-restraints excluded: chain E residue 723 LYS Chi-restraints excluded: chain E residue 730 ARG Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain P residue 105 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 68 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 146 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.0070 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS A 153 ASN E 56 HIS E 153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.174063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125724 restraints weight = 42038.944| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.87 r_work: 0.3205 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13618 Z= 0.123 Angle : 0.621 13.223 18493 Z= 0.309 Chirality : 0.044 0.201 1994 Planarity : 0.004 0.049 2366 Dihedral : 8.690 103.513 2374 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.12 % Allowed : 21.93 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.21), residues: 1613 helix: 0.64 (0.22), residues: 537 sheet: -0.13 (0.30), residues: 282 loop : -0.64 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 511 TYR 0.027 0.001 TYR E 277 PHE 0.010 0.001 PHE A 653 TRP 0.016 0.001 TRP E 421 HIS 0.005 0.001 HIS E 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (13592) covalent geometry : angle 0.58885 / 0.30 (18429) SS BOND : bond 0.00117 / 0.06 ( 2) SS BOND : angle 0.43558 / 0.27 ( 4) hydrogen bonds : bond 0.03277 / 2.10 ( 537) hydrogen bonds : angle 4.92718 / 3.58 ( 1534) metal coordination : bond 0.00257 / 0.13 ( 4) link_ALPHA1-3 : bond 0.01355 / 0.67 ( 2) link_ALPHA1-3 : angle 2.61094 / 1.79 ( 6) link_ALPHA1-6 : bond 0.00433 / 0.22 ( 2) link_ALPHA1-6 : angle 1.86750 / 1.55 ( 6) link_BETA1-4 : bond 0.00916 / 0.69 ( 10) link_BETA1-4 : angle 2.11647 / 1.53 ( 30) link_NAG-ASN : bond 0.00702 / 0.49 ( 6) link_NAG-ASN : angle 5.47145 / 3.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 0.438 Fit side-chains REVERT: A 68 GLU cc_start: 0.5911 (OUTLIER) cc_final: 0.5679 (tp30) REVERT: A 495 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: A 716 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7739 (mm-30) REVERT: A 730 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7735 (ttp-110) REVERT: E 68 GLU cc_start: 0.5857 (mp0) cc_final: 0.5371 (tm-30) REVERT: E 716 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: E 723 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7506 (mtpp) REVERT: E 730 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7938 (ttp-110) outliers start: 43 outliers final: 32 residues processed: 156 average time/residue: 0.5504 time to fit residues: 94.2510 Evaluate side-chains 160 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain E residue 530 ILE Chi-restraints excluded: chain E residue 554 SER Chi-restraints excluded: chain E residue 618 HIS Chi-restraints excluded: chain E residue 667 GLN Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 716 GLU Chi-restraints excluded: chain E residue 723 LYS Chi-restraints excluded: chain E residue 730 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.0010 chunk 117 optimal weight: 0.6980 chunk 139 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 122 optimal weight: 0.0770 overall best weight: 0.6346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS A 153 ASN E 56 HIS E 124 HIS E 153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.175997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.128574 restraints weight = 31210.336| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.27 r_work: 0.3267 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13618 Z= 0.107 Angle : 0.582 11.225 18493 Z= 0.291 Chirality : 0.043 0.181 1994 Planarity : 0.004 0.051 2366 Dihedral : 8.250 103.136 2372 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.12 % Allowed : 22.08 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.21), residues: 1613 helix: 1.05 (0.23), residues: 527 sheet: -0.06 (0.30), residues: 286 loop : -0.59 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 511 TYR 0.026 0.001 TYR E 277 PHE 0.012 0.001 PHE A 653 TRP 0.015 0.001 TRP E 421 HIS 0.004 0.001 HIS E 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (13592) covalent geometry : angle 0.55757 / 0.29 (18429) SS BOND : bond 0.00108 / 0.06 ( 2) SS BOND : angle 0.43196 / 0.26 ( 4) hydrogen bonds : bond 0.03030 / 1.94 ( 537) hydrogen bonds : angle 4.77128 / 3.46 ( 1534) metal coordination : bond 0.00174 / 0.09 ( 4) link_ALPHA1-3 : bond 0.01254 / 0.62 ( 2) link_ALPHA1-3 : angle 2.43402 / 1.68 ( 6) link_ALPHA1-6 : bond 0.00442 / 0.22 ( 2) link_ALPHA1-6 : angle 1.67956 / 1.39 ( 6) link_BETA1-4 : bond 0.00886 / 0.65 ( 10) link_BETA1-4 : angle 2.03218 / 1.45 ( 30) link_NAG-ASN : bond 0.00437 / 0.30 ( 6) link_NAG-ASN : angle 4.47254 / 3.13 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.382 Fit side-chains REVERT: A 68 GLU cc_start: 0.5787 (OUTLIER) cc_final: 0.5347 (tm-30) REVERT: A 495 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: A 716 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7843 (mm-30) REVERT: A 730 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7742 (ttp-110) REVERT: E 68 GLU cc_start: 0.5818 (mp0) cc_final: 0.5272 (tm-30) REVERT: E 123 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.8036 (m) REVERT: E 511 ARG cc_start: 0.7462 (tmm-80) cc_final: 0.7260 (ttt90) REVERT: E 716 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: E 723 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7394 (mtpp) REVERT: E 730 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7952 (ttp-110) outliers start: 43 outliers final: 27 residues processed: 159 average time/residue: 0.5389 time to fit residues: 94.2527 Evaluate side-chains 161 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 530 ILE Chi-restraints excluded: chain E residue 554 SER Chi-restraints excluded: chain E residue 618 HIS Chi-restraints excluded: chain E residue 667 GLN Chi-restraints excluded: chain E residue 714 ASP Chi-restraints excluded: chain E residue 716 GLU Chi-restraints excluded: chain E residue 723 LYS Chi-restraints excluded: chain E residue 730 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 0.0270 chunk 148 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN E 56 HIS E 153 ASN E 451 ASN E 589 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.171237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.134329 restraints weight = 40587.785| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 6.08 r_work: 0.3116 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13618 Z= 0.216 Angle : 0.704 13.260 18493 Z= 0.354 Chirality : 0.047 0.203 1994 Planarity : 0.005 0.049 2366 Dihedral : 8.533 98.903 2372 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.34 % Allowed : 21.64 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.21), residues: 1613 helix: 0.34 (0.21), residues: 529 sheet: -0.20 (0.30), residues: 284 loop : -0.73 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 511 TYR 0.033 0.002 TYR E 300 PHE 0.014 0.002 PHE A 737 TRP 0.014 0.002 TRP E 421 HIS 0.006 0.002 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (13592) covalent geometry : angle 0.67497 / 0.35 (18429) SS BOND : bond 0.00159 / 0.08 ( 2) SS BOND : angle 0.69580 / 0.40 ( 4) hydrogen bonds : bond 0.03976 / 2.57 ( 537) hydrogen bonds : angle 5.14241 / 3.72 ( 1534) metal coordination : bond 0.00523 / 0.26 ( 4) link_ALPHA1-3 : bond 0.01258 / 0.62 ( 2) link_ALPHA1-3 : angle 2.75938 / 1.86 ( 6) link_ALPHA1-6 : bond 0.00386 / 0.19 ( 2) link_ALPHA1-6 : angle 1.81793 / 1.57 ( 6) link_BETA1-4 : bond 0.00929 / 0.69 ( 10) link_BETA1-4 : angle 2.37890 / 1.75 ( 30) link_NAG-ASN : bond 0.00819 / 0.55 ( 6) link_NAG-ASN : angle 5.44904 / 3.94 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4710.90 seconds wall clock time: 81 minutes 6.26 seconds (4866.26 seconds total)