Starting phenix.real_space_refine on Thu Mar 21 02:13:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjt_24490/03_2024/7rjt_24490_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjt_24490/03_2024/7rjt_24490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjt_24490/03_2024/7rjt_24490.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjt_24490/03_2024/7rjt_24490.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjt_24490/03_2024/7rjt_24490_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjt_24490/03_2024/7rjt_24490_updated.pdb" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ba 9 18.26 5 K 3 8.98 5 P 4 5.49 5 S 176 5.16 5 C 18736 2.51 5 N 4768 2.21 5 O 5276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 839": "OD1" <-> "OD2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 839": "OD1" <-> "OD2" Residue "D PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 839": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28972 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7188 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 36, 'TRANS': 865} Chain breaks: 4 Chain: "B" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7188 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 36, 'TRANS': 865} Chain breaks: 4 Chain: "C" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7188 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 36, 'TRANS': 865} Chain breaks: 4 Chain: "D" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7188 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 36, 'TRANS': 865} Chain breaks: 4 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 52 Unusual residues: {' K': 3, ' BA': 3, 'PGW': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {' BA': 2, 'PGW': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {' BA': 2, 'PGW': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {' BA': 2, 'PGW': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 14.70, per 1000 atoms: 0.51 Number of scatterers: 28972 At special positions: 0 Unit cell: (172.764, 172.764, 129.287, 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) Ba 9 55.98 K 3 19.00 S 176 16.00 P 4 15.00 O 5276 8.00 N 4768 7.00 C 18736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 11.03 Conformation dependent library (CDL) restraints added in 5.6 seconds 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6808 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 164 helices and 16 sheets defined 45.6% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.29 Creating SS restraints... Processing helix chain 'A' and resid 17 through 42 removed outlier: 3.978A pdb=" N SER A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 97 through 122 Processing helix chain 'A' and resid 137 through 158 Processing helix chain 'A' and resid 163 through 166 No H-bonds generated for 'chain 'A' and resid 163 through 166' Processing helix chain 'A' and resid 170 through 188 Proline residue: A 180 - end of helix Processing helix chain 'A' and resid 196 through 213 Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 219 through 248 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.551A pdb=" N SER A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.515A pdb=" N GLY A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 399 through 402 No H-bonds generated for 'chain 'A' and resid 399 through 402' Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 453 through 459 removed outlier: 3.643A pdb=" N ALA A 456 " --> pdb=" O HIS A 453 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 458 " --> pdb=" O LYS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 513 through 522 removed outlier: 3.595A pdb=" N GLY A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 593 through 600 removed outlier: 3.683A pdb=" N LYS A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 593 through 600' Processing helix chain 'A' and resid 613 through 616 No H-bonds generated for 'chain 'A' and resid 613 through 616' Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 756 through 764 removed outlier: 4.507A pdb=" N MET A 761 " --> pdb=" O ASN A 758 " (cutoff:3.500A) Proline residue: A 762 - end of helix Processing helix chain 'A' and resid 770 through 772 No H-bonds generated for 'chain 'A' and resid 770 through 772' Processing helix chain 'A' and resid 783 through 791 removed outlier: 4.654A pdb=" N LYS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N THR A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 813 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 840 through 851 Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.874A pdb=" N VAL A 898 " --> pdb=" O ASP A 895 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN A 899 " --> pdb=" O SER A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 917 through 920 No H-bonds generated for 'chain 'A' and resid 917 through 920' Processing helix chain 'A' and resid 927 through 939 removed outlier: 3.763A pdb=" N SER A 932 " --> pdb=" O VAL A 929 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET A 934 " --> pdb=" O ASP A 931 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 935 " --> pdb=" O SER A 932 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR A 936 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 937 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 952 Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.675A pdb=" N GLU A 965 " --> pdb=" O GLN A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 981 Processing helix chain 'A' and resid 998 through 1000 No H-bonds generated for 'chain 'A' and resid 998 through 1000' Processing helix chain 'A' and resid 1006 through 1016 Processing helix chain 'B' and resid 17 through 42 removed outlier: 3.978A pdb=" N SER B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 97 through 122 Processing helix chain 'B' and resid 137 through 158 Processing helix chain 'B' and resid 163 through 166 No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 170 through 188 Proline residue: B 180 - end of helix Processing helix chain 'B' and resid 196 through 213 Proline residue: B 207 - end of helix Processing helix chain 'B' and resid 219 through 248 Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 287 through 306 removed outlier: 3.551A pdb=" N SER B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.515A pdb=" N GLY B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 374 through 382 Processing helix chain 'B' and resid 399 through 402 No H-bonds generated for 'chain 'B' and resid 399 through 402' Processing helix chain 'B' and resid 422 through 439 Processing helix chain 'B' and resid 453 through 459 removed outlier: 3.644A pdb=" N ALA B 456 " --> pdb=" O HIS B 453 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 458 " --> pdb=" O LYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 468 No H-bonds generated for 'chain 'B' and resid 466 through 468' Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 513 through 522 removed outlier: 3.595A pdb=" N GLY B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 540 through 549 Processing helix chain 'B' and resid 593 through 600 removed outlier: 3.683A pdb=" N LYS B 597 " --> pdb=" O ALA B 593 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 593 through 600' Processing helix chain 'B' and resid 613 through 616 No H-bonds generated for 'chain 'B' and resid 613 through 616' Processing helix chain 'B' and resid 722 through 724 No H-bonds generated for 'chain 'B' and resid 722 through 724' Processing helix chain 'B' and resid 729 through 734 Processing helix chain 'B' and resid 756 through 764 removed outlier: 4.507A pdb=" N MET B 761 " --> pdb=" O ASN B 758 " (cutoff:3.500A) Proline residue: B 762 - end of helix Processing helix chain 'B' and resid 770 through 772 No H-bonds generated for 'chain 'B' and resid 770 through 772' Processing helix chain 'B' and resid 783 through 791 removed outlier: 4.654A pdb=" N LYS B 790 " --> pdb=" O HIS B 786 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N THR B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 835 through 837 No H-bonds generated for 'chain 'B' and resid 835 through 837' Processing helix chain 'B' and resid 840 through 851 Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.875A pdb=" N VAL B 898 " --> pdb=" O ASP B 895 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN B 899 " --> pdb=" O SER B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 915 No H-bonds generated for 'chain 'B' and resid 913 through 915' Processing helix chain 'B' and resid 917 through 920 No H-bonds generated for 'chain 'B' and resid 917 through 920' Processing helix chain 'B' and resid 927 through 939 removed outlier: 3.763A pdb=" N SER B 932 " --> pdb=" O VAL B 929 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET B 934 " --> pdb=" O ASP B 931 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B 935 " --> pdb=" O SER B 932 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR B 936 " --> pdb=" O LEU B 933 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 937 " --> pdb=" O MET B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 952 Processing helix chain 'B' and resid 957 through 965 removed outlier: 3.675A pdb=" N GLU B 965 " --> pdb=" O GLN B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 981 Processing helix chain 'B' and resid 998 through 1000 No H-bonds generated for 'chain 'B' and resid 998 through 1000' Processing helix chain 'B' and resid 1006 through 1016 Processing helix chain 'C' and resid 17 through 42 removed outlier: 3.978A pdb=" N SER C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER C 23 " --> pdb=" O PHE C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 92 Processing helix chain 'C' and resid 97 through 122 Processing helix chain 'C' and resid 137 through 158 Processing helix chain 'C' and resid 163 through 166 No H-bonds generated for 'chain 'C' and resid 163 through 166' Processing helix chain 'C' and resid 170 through 188 Proline residue: C 180 - end of helix Processing helix chain 'C' and resid 196 through 213 Proline residue: C 207 - end of helix Processing helix chain 'C' and resid 219 through 248 Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 287 through 306 removed outlier: 3.551A pdb=" N SER C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.515A pdb=" N GLY C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 374 through 382 Processing helix chain 'C' and resid 399 through 402 No H-bonds generated for 'chain 'C' and resid 399 through 402' Processing helix chain 'C' and resid 422 through 439 Processing helix chain 'C' and resid 453 through 459 removed outlier: 3.644A pdb=" N ALA C 456 " --> pdb=" O HIS C 453 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 458 " --> pdb=" O LYS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 468 No H-bonds generated for 'chain 'C' and resid 466 through 468' Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 492 through 499 Processing helix chain 'C' and resid 513 through 522 removed outlier: 3.595A pdb=" N GLY C 521 " --> pdb=" O ASP C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 535 No H-bonds generated for 'chain 'C' and resid 533 through 535' Processing helix chain 'C' and resid 540 through 549 Processing helix chain 'C' and resid 593 through 600 removed outlier: 3.683A pdb=" N LYS C 597 " --> pdb=" O ALA C 593 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 593 through 600' Processing helix chain 'C' and resid 613 through 616 No H-bonds generated for 'chain 'C' and resid 613 through 616' Processing helix chain 'C' and resid 722 through 724 No H-bonds generated for 'chain 'C' and resid 722 through 724' Processing helix chain 'C' and resid 729 through 734 Processing helix chain 'C' and resid 756 through 764 removed outlier: 4.507A pdb=" N MET C 761 " --> pdb=" O ASN C 758 " (cutoff:3.500A) Proline residue: C 762 - end of helix Processing helix chain 'C' and resid 770 through 772 No H-bonds generated for 'chain 'C' and resid 770 through 772' Processing helix chain 'C' and resid 783 through 791 removed outlier: 4.655A pdb=" N LYS C 790 " --> pdb=" O HIS C 786 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N THR C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 813 Processing helix chain 'C' and resid 835 through 837 No H-bonds generated for 'chain 'C' and resid 835 through 837' Processing helix chain 'C' and resid 840 through 851 Processing helix chain 'C' and resid 895 through 900 removed outlier: 3.874A pdb=" N VAL C 898 " --> pdb=" O ASP C 895 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN C 899 " --> pdb=" O SER C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 915 No H-bonds generated for 'chain 'C' and resid 913 through 915' Processing helix chain 'C' and resid 917 through 920 No H-bonds generated for 'chain 'C' and resid 917 through 920' Processing helix chain 'C' and resid 927 through 939 removed outlier: 3.763A pdb=" N SER C 932 " --> pdb=" O VAL C 929 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET C 934 " --> pdb=" O ASP C 931 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 935 " --> pdb=" O SER C 932 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR C 936 " --> pdb=" O LEU C 933 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER C 937 " --> pdb=" O MET C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 952 Processing helix chain 'C' and resid 957 through 965 removed outlier: 3.675A pdb=" N GLU C 965 " --> pdb=" O GLN C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 981 Processing helix chain 'C' and resid 998 through 1000 No H-bonds generated for 'chain 'C' and resid 998 through 1000' Processing helix chain 'C' and resid 1006 through 1016 Processing helix chain 'D' and resid 17 through 42 removed outlier: 3.978A pdb=" N SER D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER D 23 " --> pdb=" O PHE D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 97 through 122 Processing helix chain 'D' and resid 137 through 158 Processing helix chain 'D' and resid 163 through 166 No H-bonds generated for 'chain 'D' and resid 163 through 166' Processing helix chain 'D' and resid 170 through 188 Proline residue: D 180 - end of helix Processing helix chain 'D' and resid 196 through 213 Proline residue: D 207 - end of helix Processing helix chain 'D' and resid 219 through 248 Processing helix chain 'D' and resid 263 through 274 Processing helix chain 'D' and resid 287 through 306 removed outlier: 3.551A pdb=" N SER D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 removed outlier: 3.515A pdb=" N GLY D 316 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 Processing helix chain 'D' and resid 374 through 382 Processing helix chain 'D' and resid 399 through 402 No H-bonds generated for 'chain 'D' and resid 399 through 402' Processing helix chain 'D' and resid 422 through 439 Processing helix chain 'D' and resid 453 through 459 removed outlier: 3.643A pdb=" N ALA D 456 " --> pdb=" O HIS D 453 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 458 " --> pdb=" O LYS D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 468 No H-bonds generated for 'chain 'D' and resid 466 through 468' Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 492 through 499 Processing helix chain 'D' and resid 513 through 522 removed outlier: 3.595A pdb=" N GLY D 521 " --> pdb=" O ASP D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 540 through 549 Processing helix chain 'D' and resid 593 through 600 removed outlier: 3.683A pdb=" N LYS D 597 " --> pdb=" O ALA D 593 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 593 through 600' Processing helix chain 'D' and resid 613 through 616 No H-bonds generated for 'chain 'D' and resid 613 through 616' Processing helix chain 'D' and resid 722 through 724 No H-bonds generated for 'chain 'D' and resid 722 through 724' Processing helix chain 'D' and resid 729 through 734 Processing helix chain 'D' and resid 756 through 764 removed outlier: 4.507A pdb=" N MET D 761 " --> pdb=" O ASN D 758 " (cutoff:3.500A) Proline residue: D 762 - end of helix Processing helix chain 'D' and resid 770 through 772 No H-bonds generated for 'chain 'D' and resid 770 through 772' Processing helix chain 'D' and resid 783 through 791 removed outlier: 4.655A pdb=" N LYS D 790 " --> pdb=" O HIS D 786 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N THR D 791 " --> pdb=" O ARG D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 813 Processing helix chain 'D' and resid 835 through 837 No H-bonds generated for 'chain 'D' and resid 835 through 837' Processing helix chain 'D' and resid 840 through 851 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.874A pdb=" N VAL D 898 " --> pdb=" O ASP D 895 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN D 899 " --> pdb=" O SER D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 915 No H-bonds generated for 'chain 'D' and resid 913 through 915' Processing helix chain 'D' and resid 917 through 920 No H-bonds generated for 'chain 'D' and resid 917 through 920' Processing helix chain 'D' and resid 927 through 939 removed outlier: 3.763A pdb=" N SER D 932 " --> pdb=" O VAL D 929 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET D 934 " --> pdb=" O ASP D 931 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 935 " --> pdb=" O SER D 932 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR D 936 " --> pdb=" O LEU D 933 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER D 937 " --> pdb=" O MET D 934 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 952 Processing helix chain 'D' and resid 957 through 965 removed outlier: 3.675A pdb=" N GLU D 965 " --> pdb=" O GLN D 961 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 981 Processing helix chain 'D' and resid 998 through 1000 No H-bonds generated for 'chain 'D' and resid 998 through 1000' Processing helix chain 'D' and resid 1006 through 1016 Processing sheet with id= A, first strand: chain 'A' and resid 471 through 474 removed outlier: 4.144A pdb=" N ALA A 410 " --> pdb=" O HIS A 333 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 525 through 530 removed outlier: 5.088A pdb=" N GLN A 585 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 557 " --> pdb=" O PHE A 587 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE A 589 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 555 " --> pdb=" O ILE A 589 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 924 through 926 removed outlier: 8.252A pdb=" N PHE A 925 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR A 890 " --> pdb=" O PHE A 925 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS A 822 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLU A 891 " --> pdb=" O CYS A 822 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE A 824 " --> pdb=" O GLU A 891 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 780 " --> pdb=" O LEU A 801 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 986 through 991 removed outlier: 3.943A pdb=" N GLY A1023 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A1062 " --> pdb=" O CYS A1021 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS A1021 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 471 through 474 removed outlier: 4.144A pdb=" N ALA B 410 " --> pdb=" O HIS B 333 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 525 through 530 removed outlier: 5.088A pdb=" N GLN B 585 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 557 " --> pdb=" O PHE B 587 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE B 589 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU B 555 " --> pdb=" O ILE B 589 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 924 through 926 removed outlier: 8.252A pdb=" N PHE B 925 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR B 890 " --> pdb=" O PHE B 925 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N CYS B 822 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLU B 891 " --> pdb=" O CYS B 822 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE B 824 " --> pdb=" O GLU B 891 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY B 780 " --> pdb=" O LEU B 801 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 986 through 991 removed outlier: 3.943A pdb=" N GLY B1023 " --> pdb=" O TYR B1060 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU B1062 " --> pdb=" O CYS B1021 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS B1021 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 471 through 474 removed outlier: 4.144A pdb=" N ALA C 410 " --> pdb=" O HIS C 333 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 525 through 530 removed outlier: 5.088A pdb=" N GLN C 585 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA C 557 " --> pdb=" O PHE C 587 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE C 589 " --> pdb=" O LEU C 555 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU C 555 " --> pdb=" O ILE C 589 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 924 through 926 removed outlier: 8.252A pdb=" N PHE C 925 " --> pdb=" O LEU C 888 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR C 890 " --> pdb=" O PHE C 925 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS C 822 " --> pdb=" O ILE C 889 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLU C 891 " --> pdb=" O CYS C 822 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE C 824 " --> pdb=" O GLU C 891 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY C 780 " --> pdb=" O LEU C 801 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 986 through 991 removed outlier: 3.943A pdb=" N GLY C1023 " --> pdb=" O TYR C1060 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU C1062 " --> pdb=" O CYS C1021 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS C1021 " --> pdb=" O LEU C1062 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 471 through 474 removed outlier: 4.144A pdb=" N ALA D 410 " --> pdb=" O HIS D 333 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 525 through 530 removed outlier: 5.088A pdb=" N GLN D 585 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D 557 " --> pdb=" O PHE D 587 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE D 589 " --> pdb=" O LEU D 555 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU D 555 " --> pdb=" O ILE D 589 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 924 through 926 removed outlier: 8.252A pdb=" N PHE D 925 " --> pdb=" O LEU D 888 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR D 890 " --> pdb=" O PHE D 925 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS D 822 " --> pdb=" O ILE D 889 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLU D 891 " --> pdb=" O CYS D 822 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE D 824 " --> pdb=" O GLU D 891 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY D 780 " --> pdb=" O LEU D 801 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 986 through 991 removed outlier: 3.943A pdb=" N GLY D1023 " --> pdb=" O TYR D1060 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU D1062 " --> pdb=" O CYS D1021 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS D1021 " --> pdb=" O LEU D1062 " (cutoff:3.500A) 1136 hydrogen bonds defined for protein. 3084 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: 10.69 Time building geometry restraints manager: 11.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5773 1.33 - 1.45: 7118 1.45 - 1.57: 16437 1.57 - 1.69: 4 1.69 - 1.81: 268 Bond restraints: 29600 Sorted by residual: bond pdb=" C10 PGW B1103 " pdb=" C9 PGW B1103 " ideal model delta sigma weight residual 1.333 1.564 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C10 PGW C1103 " pdb=" C9 PGW C1103 " ideal model delta sigma weight residual 1.333 1.564 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C10 PGW A1103 " pdb=" C9 PGW A1103 " ideal model delta sigma weight residual 1.333 1.564 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C10 PGW D1103 " pdb=" C9 PGW D1103 " ideal model delta sigma weight residual 1.333 1.564 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" O14 PGW D1106 " pdb=" P PGW D1106 " ideal model delta sigma weight residual 1.512 1.731 -0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 29595 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.32: 784 106.32 - 113.24: 15770 113.24 - 120.16: 10653 120.16 - 127.07: 12585 127.07 - 133.99: 320 Bond angle restraints: 40112 Sorted by residual: angle pdb=" O12 PGW C1106 " pdb=" P PGW C1106 " pdb=" O13 PGW C1106 " ideal model delta sigma weight residual 111.13 126.94 -15.81 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O12 PGW B1106 " pdb=" P PGW B1106 " pdb=" O13 PGW B1106 " ideal model delta sigma weight residual 111.13 126.94 -15.81 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O12 PGW D1106 " pdb=" P PGW D1106 " pdb=" O13 PGW D1106 " ideal model delta sigma weight residual 111.13 126.88 -15.75 3.00e+00 1.11e-01 2.76e+01 angle pdb=" O12 PGW A1106 " pdb=" P PGW A1106 " pdb=" O13 PGW A1106 " ideal model delta sigma weight residual 111.13 126.88 -15.75 3.00e+00 1.11e-01 2.76e+01 angle pdb=" O13 PGW B1106 " pdb=" P PGW B1106 " pdb=" O14 PGW B1106 " ideal model delta sigma weight residual 119.81 104.10 15.71 3.00e+00 1.11e-01 2.74e+01 ... (remaining 40107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 15862 17.48 - 34.96: 1306 34.96 - 52.44: 260 52.44 - 69.92: 96 69.92 - 87.40: 16 Dihedral angle restraints: 17540 sinusoidal: 7008 harmonic: 10532 Sorted by residual: dihedral pdb=" CA TYR D1025 " pdb=" C TYR D1025 " pdb=" N ARG D1026 " pdb=" CA ARG D1026 " ideal model delta harmonic sigma weight residual -180.00 -156.88 -23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA TYR A1025 " pdb=" C TYR A1025 " pdb=" N ARG A1026 " pdb=" CA ARG A1026 " ideal model delta harmonic sigma weight residual -180.00 -156.88 -23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA TYR B1025 " pdb=" C TYR B1025 " pdb=" N ARG B1026 " pdb=" CA ARG B1026 " ideal model delta harmonic sigma weight residual 180.00 -156.90 -23.10 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 17537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2994 0.035 - 0.069: 1124 0.069 - 0.104: 294 0.104 - 0.138: 80 0.138 - 0.173: 8 Chirality restraints: 4500 Sorted by residual: chirality pdb=" CB ILE D 92 " pdb=" CA ILE D 92 " pdb=" CG1 ILE D 92 " pdb=" CG2 ILE D 92 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CB ILE C 92 " pdb=" CA ILE C 92 " pdb=" CG1 ILE C 92 " pdb=" CG2 ILE C 92 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CB ILE B 92 " pdb=" CA ILE B 92 " pdb=" CG1 ILE B 92 " pdb=" CG2 ILE B 92 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 4497 not shown) Planarity restraints: 5092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW C1103 " -0.024 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C10 PGW C1103 " 0.045 2.00e-02 2.50e+03 pdb=" C8 PGW C1103 " 0.023 2.00e-02 2.50e+03 pdb=" C9 PGW C1103 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B1103 " 0.023 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C10 PGW B1103 " -0.044 2.00e-02 2.50e+03 pdb=" C8 PGW B1103 " -0.023 2.00e-02 2.50e+03 pdb=" C9 PGW B1103 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D1103 " -0.023 2.00e-02 2.50e+03 3.51e-02 1.24e+01 pdb=" C10 PGW D1103 " 0.044 2.00e-02 2.50e+03 pdb=" C8 PGW D1103 " 0.023 2.00e-02 2.50e+03 pdb=" C9 PGW D1103 " -0.044 2.00e-02 2.50e+03 ... (remaining 5089 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 9112 2.83 - 3.41: 30546 3.41 - 3.98: 51904 3.98 - 4.56: 75036 4.56 - 5.14: 109755 Nonbonded interactions: 276353 Sorted by model distance: nonbonded pdb=" OH TYR D 321 " pdb=" OE2 GLU D 377 " model vdw 2.251 2.440 nonbonded pdb=" OH TYR A 321 " pdb=" OE2 GLU A 377 " model vdw 2.251 2.440 nonbonded pdb=" OH TYR C 321 " pdb=" OE2 GLU C 377 " model vdw 2.252 2.440 nonbonded pdb=" OH TYR B 321 " pdb=" OE2 GLU B 377 " model vdw 2.252 2.440 nonbonded pdb=" O SER A 463 " pdb=" NH2 ARG A 468 " model vdw 2.298 2.520 ... (remaining 276348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 1066 or resid 1101 through 1106)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.280 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 77.190 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.190 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: 0.010 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 : 0.005 0.231 29600 Z= 0.362 Angle : 0.591 15.807 40112 Z= 0.273 Chirality : 0.040 0.173 4500 Planarity : 0.003 0.035 5092 Dihedral : 14.146 87.397 10732 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3568 helix: 1.13 (0.14), residues: 1616 sheet: -0.28 (0.28), residues: 404 loop : -0.05 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 514 HIS 0.010 0.001 HIS D 786 PHE 0.013 0.001 PHE D 107 TYR 0.030 0.001 TYR C1025 ARG 0.002 0.000 ARG B1041 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 3.105 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 1.4839 time to fit residues: 284.9037 Evaluate side-chains 128 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 2.9990 chunk 272 optimal weight: 9.9990 chunk 151 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 184 optimal weight: 40.0000 chunk 145 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 109 optimal weight: 30.0000 chunk 171 optimal weight: 1.9990 chunk 210 optimal weight: 0.5980 chunk 326 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 429 ASN A 894 ASN A 897 ASN B 398 ASN B 429 ASN B 894 ASN B 897 ASN C 398 ASN C 429 ASN C 894 ASN C 897 ASN D 398 ASN D 429 ASN D 894 ASN D 897 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29600 Z= 0.293 Angle : 0.524 6.981 40112 Z= 0.260 Chirality : 0.042 0.183 4500 Planarity : 0.004 0.036 5092 Dihedral : 8.190 81.172 4024 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.02 % Allowed : 5.15 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3568 helix: 0.99 (0.13), residues: 1608 sheet: -0.33 (0.27), residues: 404 loop : -0.01 (0.17), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 514 HIS 0.006 0.001 HIS B 333 PHE 0.013 0.001 PHE D 500 TYR 0.033 0.001 TYR D1025 ARG 0.002 0.000 ARG D 503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 3.657 Fit side-chains REVERT: A 267 LEU cc_start: 0.6386 (tm) cc_final: 0.6180 (tm) REVERT: A 526 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6911 (ttp) REVERT: B 267 LEU cc_start: 0.6383 (tm) cc_final: 0.6178 (tm) REVERT: B 526 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6916 (ttp) REVERT: C 267 LEU cc_start: 0.6390 (tm) cc_final: 0.6185 (tm) REVERT: C 388 GLU cc_start: 0.6853 (mp0) cc_final: 0.6565 (mp0) REVERT: C 526 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6915 (ttp) REVERT: D 267 LEU cc_start: 0.6393 (tm) cc_final: 0.6189 (tm) REVERT: D 388 GLU cc_start: 0.6905 (mp0) cc_final: 0.6518 (mp0) REVERT: D 526 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6913 (ttp) outliers start: 32 outliers final: 4 residues processed: 146 average time/residue: 1.4633 time to fit residues: 251.5461 Evaluate side-chains 144 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 526 MET Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 526 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 30.0000 chunk 101 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 222 optimal weight: 0.7980 chunk 90 optimal weight: 100.0000 chunk 327 optimal weight: 4.9990 chunk 353 optimal weight: 0.0970 chunk 291 optimal weight: 0.1980 chunk 324 optimal weight: 0.5980 chunk 111 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 940 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29600 Z= 0.157 Angle : 0.447 6.879 40112 Z= 0.225 Chirality : 0.039 0.148 4500 Planarity : 0.003 0.036 5092 Dihedral : 7.495 84.364 4024 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.51 % Allowed : 7.62 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3568 helix: 1.04 (0.13), residues: 1632 sheet: -0.14 (0.27), residues: 404 loop : -0.11 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 514 HIS 0.002 0.001 HIS C 771 PHE 0.009 0.001 PHE B 107 TYR 0.016 0.001 TYR C1025 ARG 0.002 0.000 ARG A 757 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 3.262 Fit side-chains REVERT: A 267 LEU cc_start: 0.6349 (tm) cc_final: 0.6094 (tm) REVERT: A 526 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6946 (ttp) REVERT: B 267 LEU cc_start: 0.6344 (tm) cc_final: 0.6091 (tm) REVERT: B 526 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6951 (ttp) REVERT: C 267 LEU cc_start: 0.6351 (tm) cc_final: 0.6096 (tm) REVERT: C 526 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6955 (ttp) REVERT: D 267 LEU cc_start: 0.6357 (tm) cc_final: 0.6104 (tm) REVERT: D 526 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6947 (ttp) outliers start: 16 outliers final: 4 residues processed: 136 average time/residue: 1.5522 time to fit residues: 247.2789 Evaluate side-chains 132 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 526 MET Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 526 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 0.6980 chunk 246 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 36 optimal weight: 0.0370 chunk 156 optimal weight: 3.9990 chunk 219 optimal weight: 0.9980 chunk 328 optimal weight: 1.9990 chunk 347 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 311 optimal weight: 5.9990 chunk 93 optimal weight: 50.0000 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 940 ASN B 940 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 29600 Z= 0.144 Angle : 0.434 6.872 40112 Z= 0.219 Chirality : 0.039 0.137 4500 Planarity : 0.003 0.036 5092 Dihedral : 6.998 85.265 4024 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.89 % Allowed : 8.89 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3568 helix: 1.13 (0.13), residues: 1636 sheet: -0.02 (0.28), residues: 404 loop : -0.05 (0.17), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 514 HIS 0.002 0.000 HIS C 771 PHE 0.008 0.001 PHE A 107 TYR 0.013 0.001 TYR D1025 ARG 0.002 0.000 ARG B 757 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 3.183 Fit side-chains REVERT: A 267 LEU cc_start: 0.6412 (tm) cc_final: 0.6175 (tm) REVERT: A 895 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6848 (p0) REVERT: B 267 LEU cc_start: 0.6411 (tm) cc_final: 0.6175 (tm) REVERT: B 895 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6849 (p0) REVERT: C 267 LEU cc_start: 0.6416 (tm) cc_final: 0.6164 (tm) REVERT: C 895 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6845 (p0) REVERT: D 267 LEU cc_start: 0.6424 (tm) cc_final: 0.6187 (tm) REVERT: D 895 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6851 (p0) outliers start: 28 outliers final: 4 residues processed: 143 average time/residue: 1.3492 time to fit residues: 229.5331 Evaluate side-chains 143 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 895 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 50.0000 chunk 197 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 259 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 chunk 0 optimal weight: 100.0000 chunk 177 optimal weight: 0.6980 chunk 312 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 HIS B 453 HIS C 453 HIS D 453 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 29600 Z= 0.132 Angle : 0.428 6.882 40112 Z= 0.216 Chirality : 0.038 0.131 4500 Planarity : 0.003 0.035 5092 Dihedral : 6.578 86.305 4024 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.76 % Allowed : 10.23 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3568 helix: 1.07 (0.13), residues: 1680 sheet: 0.08 (0.28), residues: 404 loop : -0.14 (0.17), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 391 HIS 0.002 0.000 HIS D 771 PHE 0.007 0.001 PHE A 107 TYR 0.011 0.001 TYR D1025 ARG 0.002 0.000 ARG C 757 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 3.383 Fit side-chains REVERT: A 267 LEU cc_start: 0.6419 (tm) cc_final: 0.6154 (tm) REVERT: A 494 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8449 (p) REVERT: A 895 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6822 (p0) REVERT: B 267 LEU cc_start: 0.6418 (tm) cc_final: 0.6155 (tm) REVERT: B 494 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8451 (p) REVERT: B 895 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6821 (p0) REVERT: C 267 LEU cc_start: 0.6427 (tm) cc_final: 0.6163 (tm) REVERT: C 494 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8452 (p) REVERT: C 895 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6816 (p0) REVERT: D 267 LEU cc_start: 0.6430 (tm) cc_final: 0.6165 (tm) REVERT: D 494 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8454 (p) REVERT: D 895 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6816 (p0) outliers start: 24 outliers final: 4 residues processed: 149 average time/residue: 1.3470 time to fit residues: 239.3615 Evaluate side-chains 142 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 895 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 348 optimal weight: 0.6980 chunk 289 optimal weight: 0.0270 chunk 161 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 182 optimal weight: 40.0000 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN B 398 ASN C 398 ASN D 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29600 Z= 0.215 Angle : 0.462 6.887 40112 Z= 0.232 Chirality : 0.040 0.134 4500 Planarity : 0.003 0.036 5092 Dihedral : 6.211 87.485 4024 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.37 % Allowed : 10.90 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3568 helix: 1.21 (0.13), residues: 1612 sheet: 0.01 (0.27), residues: 404 loop : 0.01 (0.17), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 391 HIS 0.004 0.001 HIS C 333 PHE 0.009 0.001 PHE C 500 TYR 0.014 0.001 TYR C1025 ARG 0.002 0.000 ARG C 757 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 137 time to evaluate : 3.004 Fit side-chains REVERT: A 267 LEU cc_start: 0.6603 (tm) cc_final: 0.6366 (tm) REVERT: A 388 GLU cc_start: 0.6798 (mp0) cc_final: 0.6420 (mp0) REVERT: A 494 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8532 (p) REVERT: A 891 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6137 (tt0) REVERT: A 895 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6846 (p0) REVERT: B 267 LEU cc_start: 0.6600 (tm) cc_final: 0.6365 (tm) REVERT: B 388 GLU cc_start: 0.6793 (mp0) cc_final: 0.6417 (mp0) REVERT: B 494 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8535 (p) REVERT: B 891 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6153 (tt0) REVERT: B 895 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6845 (p0) REVERT: C 267 LEU cc_start: 0.6606 (tm) cc_final: 0.6368 (tm) REVERT: C 300 PHE cc_start: 0.8181 (m-80) cc_final: 0.7946 (t80) REVERT: C 388 GLU cc_start: 0.6795 (mp0) cc_final: 0.6419 (mp0) REVERT: C 494 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8533 (p) REVERT: C 891 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6154 (tt0) REVERT: C 895 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6830 (p0) REVERT: D 267 LEU cc_start: 0.6612 (tm) cc_final: 0.6374 (tm) REVERT: D 388 GLU cc_start: 0.6794 (mp0) cc_final: 0.6420 (mp0) REVERT: D 494 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8530 (p) REVERT: D 891 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6137 (tt0) REVERT: D 895 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6845 (p0) outliers start: 43 outliers final: 12 residues processed: 165 average time/residue: 1.5814 time to fit residues: 312.8268 Evaluate side-chains 150 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 468 ARG Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 891 GLU Chi-restraints excluded: chain D residue 895 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 198 optimal weight: 30.0000 chunk 254 optimal weight: 0.0570 chunk 197 optimal weight: 6.9990 chunk 293 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 346 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN B 398 ASN C 398 ASN D 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 29600 Z= 0.144 Angle : 0.434 6.891 40112 Z= 0.219 Chirality : 0.038 0.130 4500 Planarity : 0.003 0.035 5092 Dihedral : 5.854 88.215 4024 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.83 % Allowed : 11.72 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3568 helix: 1.03 (0.13), residues: 1704 sheet: 0.17 (0.28), residues: 404 loop : -0.13 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 514 HIS 0.002 0.000 HIS A 771 PHE 0.010 0.001 PHE D 304 TYR 0.010 0.001 TYR D1025 ARG 0.002 0.000 ARG C 757 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 3.584 Fit side-chains REVERT: A 494 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8498 (p) REVERT: A 891 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6082 (tt0) REVERT: A 907 ASP cc_start: 0.8662 (m-30) cc_final: 0.8322 (t70) REVERT: B 494 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8496 (p) REVERT: B 891 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6097 (tt0) REVERT: B 907 ASP cc_start: 0.8662 (m-30) cc_final: 0.8321 (t70) REVERT: C 494 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8498 (p) REVERT: C 891 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6101 (tt0) REVERT: D 494 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8502 (p) REVERT: D 891 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6083 (tt0) REVERT: D 907 ASP cc_start: 0.8653 (m-30) cc_final: 0.8310 (t70) outliers start: 26 outliers final: 6 residues processed: 151 average time/residue: 1.3947 time to fit residues: 249.6473 Evaluate side-chains 138 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 468 ARG Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 891 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 104 optimal weight: 40.0000 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 236 optimal weight: 0.0000 chunk 171 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 overall best weight: 1.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN B 398 ASN C 398 ASN D 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29600 Z= 0.215 Angle : 0.472 9.492 40112 Z= 0.234 Chirality : 0.040 0.132 4500 Planarity : 0.003 0.035 5092 Dihedral : 5.689 89.080 4024 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.95 % Allowed : 11.88 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3568 helix: 1.24 (0.13), residues: 1612 sheet: 0.11 (0.27), residues: 404 loop : 0.03 (0.17), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 391 HIS 0.004 0.001 HIS B 333 PHE 0.015 0.001 PHE D 300 TYR 0.013 0.001 TYR D1025 ARG 0.002 0.000 ARG C 757 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 3.291 Fit side-chains REVERT: A 300 PHE cc_start: 0.6768 (t80) cc_final: 0.6260 (t80) REVERT: A 388 GLU cc_start: 0.6794 (mp0) cc_final: 0.6405 (mp0) REVERT: A 494 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8532 (p) REVERT: A 891 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6133 (tt0) REVERT: A 907 ASP cc_start: 0.8713 (m-30) cc_final: 0.8387 (t70) REVERT: B 300 PHE cc_start: 0.6773 (t80) cc_final: 0.6263 (t80) REVERT: B 388 GLU cc_start: 0.6790 (mp0) cc_final: 0.6401 (mp0) REVERT: B 494 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8535 (p) REVERT: B 891 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6146 (tt0) REVERT: B 907 ASP cc_start: 0.8706 (m-30) cc_final: 0.8366 (t70) REVERT: C 388 GLU cc_start: 0.6792 (mp0) cc_final: 0.6405 (mp0) REVERT: C 494 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8533 (p) REVERT: C 891 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6153 (tt0) REVERT: C 895 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6828 (p0) REVERT: D 300 PHE cc_start: 0.6766 (t80) cc_final: 0.6247 (t80) REVERT: D 388 GLU cc_start: 0.6791 (mp0) cc_final: 0.6403 (mp0) REVERT: D 494 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8534 (p) REVERT: D 891 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6130 (tt0) REVERT: D 907 ASP cc_start: 0.8698 (m-30) cc_final: 0.8358 (t70) outliers start: 30 outliers final: 9 residues processed: 158 average time/residue: 1.5859 time to fit residues: 292.6650 Evaluate side-chains 151 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 468 ARG Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 891 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 0.0010 chunk 332 optimal weight: 0.9980 chunk 303 optimal weight: 0.0470 chunk 323 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 253 optimal weight: 0.5980 chunk 99 optimal weight: 20.0000 chunk 292 optimal weight: 0.2980 chunk 305 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 overall best weight: 0.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN B 398 ASN C 398 ASN D 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 29600 Z= 0.108 Angle : 0.429 7.653 40112 Z= 0.216 Chirality : 0.038 0.128 4500 Planarity : 0.003 0.035 5092 Dihedral : 5.382 89.804 4024 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.60 % Allowed : 12.36 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3568 helix: 1.12 (0.13), residues: 1704 sheet: 0.30 (0.28), residues: 404 loop : -0.06 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 514 HIS 0.002 0.000 HIS C 771 PHE 0.023 0.001 PHE C 300 TYR 0.007 0.001 TYR B1025 ARG 0.003 0.000 ARG C 757 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 2.767 Fit side-chains REVERT: A 300 PHE cc_start: 0.6795 (t80) cc_final: 0.6506 (t80) REVERT: A 494 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8416 (p) REVERT: A 907 ASP cc_start: 0.8570 (m-30) cc_final: 0.8324 (t70) REVERT: B 300 PHE cc_start: 0.6798 (t80) cc_final: 0.6505 (t80) REVERT: B 494 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8419 (p) REVERT: B 907 ASP cc_start: 0.8567 (m-30) cc_final: 0.8318 (t70) REVERT: C 494 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8419 (p) REVERT: C 895 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6812 (p0) REVERT: D 300 PHE cc_start: 0.6720 (t80) cc_final: 0.6419 (t80) REVERT: D 494 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8421 (p) REVERT: D 907 ASP cc_start: 0.8556 (m-30) cc_final: 0.8307 (t70) outliers start: 19 outliers final: 10 residues processed: 157 average time/residue: 1.3647 time to fit residues: 253.9414 Evaluate side-chains 151 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 494 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 7.9990 chunk 341 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 162 optimal weight: 0.2980 chunk 237 optimal weight: 0.1980 chunk 358 optimal weight: 0.9990 chunk 330 optimal weight: 1.9990 chunk 285 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN B 398 ASN C 398 ASN D 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 29600 Z= 0.155 Angle : 0.458 7.812 40112 Z= 0.230 Chirality : 0.039 0.133 4500 Planarity : 0.003 0.035 5092 Dihedral : 5.321 89.480 4024 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.79 % Allowed : 12.33 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 3568 helix: 1.13 (0.13), residues: 1704 sheet: 0.27 (0.28), residues: 404 loop : -0.07 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 235 HIS 0.002 0.001 HIS B 333 PHE 0.015 0.001 PHE C 300 TYR 0.014 0.001 TYR B1064 ARG 0.002 0.000 ARG B 757 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 3.637 Fit side-chains revert: symmetry clash REVERT: A 388 GLU cc_start: 0.6688 (mp0) cc_final: 0.6342 (mp0) REVERT: A 494 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8455 (p) REVERT: A 832 MET cc_start: 0.6664 (mpp) cc_final: 0.6233 (mmm) REVERT: A 895 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6867 (p0) REVERT: A 907 ASP cc_start: 0.8601 (m-30) cc_final: 0.8361 (t70) REVERT: B 388 GLU cc_start: 0.6681 (mp0) cc_final: 0.6337 (mp0) REVERT: B 494 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8454 (p) REVERT: B 832 MET cc_start: 0.6658 (mpp) cc_final: 0.6227 (mmm) REVERT: B 895 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6866 (p0) REVERT: B 907 ASP cc_start: 0.8600 (m-30) cc_final: 0.8357 (t70) REVERT: C 388 GLU cc_start: 0.6684 (mp0) cc_final: 0.6339 (mp0) REVERT: C 494 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8455 (p) REVERT: C 761 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8085 (mmm) REVERT: C 832 MET cc_start: 0.6679 (mpp) cc_final: 0.6247 (mmm) REVERT: C 895 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6816 (p0) REVERT: D 388 GLU cc_start: 0.6685 (mp0) cc_final: 0.6339 (mp0) REVERT: D 494 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8459 (p) REVERT: D 832 MET cc_start: 0.6617 (mpp) cc_final: 0.6177 (mmm) REVERT: D 895 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6864 (p0) REVERT: D 907 ASP cc_start: 0.8590 (m-30) cc_final: 0.8351 (t70) outliers start: 25 outliers final: 12 residues processed: 160 average time/residue: 1.4680 time to fit residues: 276.6432 Evaluate side-chains 161 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 524 MET Chi-restraints excluded: chain C residue 761 MET Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 895 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 3.9990 chunk 304 optimal weight: 0.9990 chunk 87 optimal weight: 0.0010 chunk 263 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 286 optimal weight: 0.0670 chunk 119 optimal weight: 0.0870 chunk 293 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 overall best weight: 0.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN B 398 ASN C 398 ASN D 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.193025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.115619 restraints weight = 37418.596| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.61 r_work: 0.3289 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 29600 Z= 0.105 Angle : 0.433 7.732 40112 Z= 0.219 Chirality : 0.038 0.125 4500 Planarity : 0.003 0.035 5092 Dihedral : 5.107 88.516 4024 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.76 % Allowed : 12.61 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.15), residues: 3568 helix: 1.23 (0.13), residues: 1700 sheet: 0.35 (0.28), residues: 416 loop : 0.04 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 514 HIS 0.002 0.000 HIS C 771 PHE 0.015 0.001 PHE C 300 TYR 0.024 0.001 TYR B 784 ARG 0.002 0.000 ARG D 757 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7321.94 seconds wall clock time: 131 minutes 50.97 seconds (7910.97 seconds total)