Starting phenix.real_space_refine on Sat Aug 10 20:24:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8y_44362/08_2024/9b8y_44362.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8y_44362/08_2024/9b8y_44362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8y_44362/08_2024/9b8y_44362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8y_44362/08_2024/9b8y_44362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8y_44362/08_2024/9b8y_44362.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8y_44362/08_2024/9b8y_44362.cif" } resolution = 3.2 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= 0.002 sd= 0.016 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 V 40 8.30 5 S 152 5.16 5 C 19340 2.51 5 N 5232 2.21 5 O 5208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29980 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7455 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 42, 'TRANS': 935} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 16, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 7455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7455 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 42, 'TRANS': 935} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 16, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 228 Chain: "C" Number of atoms: 7455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7455 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 42, 'TRANS': 935} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 16, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 228 Chain: "D" Number of atoms: 7455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7455 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 42, 'TRANS': 935} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 16, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 228 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' CA': 2, 'DVT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' CA': 2, 'DVT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' CA': 2, 'DVT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' CA': 2, 'DVT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 17.49, per 1000 atoms: 0.58 Number of scatterers: 29980 At special positions: 0 Unit cell: (158.148, 158.148, 148.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 40 22.97 Ca 8 19.99 S 152 16.00 O 5208 8.00 N 5232 7.00 C 19340 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: 15.16 Conformation dependent library (CDL) restraints added in 5.8 seconds 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7264 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 16 sheets defined 67.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.799A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.844A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 removed outlier: 3.550A pdb=" N ARG A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.540A pdb=" N ILE A 201 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.798A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.504A pdb=" N ARG A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 357 removed outlier: 4.051A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 393 through 403 Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.555A pdb=" N MET A 581 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 Processing helix chain 'A' and resid 607 through 634 Processing helix chain 'A' and resid 634 through 644 removed outlier: 3.796A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A 644 " --> pdb=" O ARG A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 removed outlier: 3.618A pdb=" N PHE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 767 through 778 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 834 Processing helix chain 'A' and resid 852 through 861 Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 906 Processing helix chain 'A' and resid 907 through 913 Processing helix chain 'A' and resid 916 through 953 removed outlier: 3.792A pdb=" N ILE A 920 " --> pdb=" O LEU A 916 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 929 " --> pdb=" O LYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 4.825A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.928A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1050 Processing helix chain 'A' and resid 1053 through 1071 removed outlier: 3.966A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.239A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1142 Processing helix chain 'A' and resid 1143 through 1172 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.799A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 removed outlier: 3.844A pdb=" N VAL B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 removed outlier: 3.550A pdb=" N ARG B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.540A pdb=" N ILE B 201 " --> pdb=" O ASP B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.798A pdb=" N GLY B 268 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 308 through 317 Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.504A pdb=" N ARG B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 4.051A pdb=" N GLN B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 425 through 435 Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 503 through 512 Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 571 through 581 removed outlier: 3.555A pdb=" N MET B 581 " --> pdb=" O TYR B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 603 Processing helix chain 'B' and resid 607 through 634 Processing helix chain 'B' and resid 634 through 644 removed outlier: 3.796A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 644 " --> pdb=" O ARG B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.617A pdb=" N PHE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 767 through 778 Processing helix chain 'B' and resid 778 through 803 Processing helix chain 'B' and resid 811 through 834 Processing helix chain 'B' and resid 852 through 861 Processing helix chain 'B' and resid 862 through 884 Processing helix chain 'B' and resid 887 through 906 Processing helix chain 'B' and resid 907 through 913 Processing helix chain 'B' and resid 916 through 953 removed outlier: 3.792A pdb=" N ILE B 920 " --> pdb=" O LEU B 916 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS B 928 " --> pdb=" O SER B 924 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP B 929 " --> pdb=" O LYS B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 974 removed outlier: 4.825A pdb=" N ARG B 969 " --> pdb=" O ARG B 965 " (cutoff:3.500A) Proline residue: B 970 - end of helix Processing helix chain 'B' and resid 979 through 983 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.929A pdb=" N VAL B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1050 Processing helix chain 'B' and resid 1053 through 1071 removed outlier: 3.966A pdb=" N SER B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1078 No H-bonds generated for 'chain 'B' and resid 1076 through 1078' Processing helix chain 'B' and resid 1079 through 1088 removed outlier: 4.239A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1142 Processing helix chain 'B' and resid 1143 through 1172 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 98 through 109 removed outlier: 3.799A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 150 removed outlier: 3.843A pdb=" N VAL C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 177 removed outlier: 3.550A pdb=" N ARG C 164 " --> pdb=" O THR C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.540A pdb=" N ILE C 201 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.798A pdb=" N GLY C 268 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 308 through 317 Processing helix chain 'C' and resid 329 through 337 removed outlier: 3.503A pdb=" N ARG C 337 " --> pdb=" O ASP C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 357 removed outlier: 4.051A pdb=" N GLN C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 393 through 403 Processing helix chain 'C' and resid 405 through 412 Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 503 through 512 Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 571 through 581 removed outlier: 3.556A pdb=" N MET C 581 " --> pdb=" O TYR C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 603 Processing helix chain 'C' and resid 607 through 634 Processing helix chain 'C' and resid 634 through 644 removed outlier: 3.795A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG C 644 " --> pdb=" O ARG C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 removed outlier: 3.619A pdb=" N PHE C 698 " --> pdb=" O VAL C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 705 Processing helix chain 'C' and resid 767 through 778 Processing helix chain 'C' and resid 778 through 803 Processing helix chain 'C' and resid 811 through 834 Processing helix chain 'C' and resid 852 through 861 Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 906 Processing helix chain 'C' and resid 907 through 913 Processing helix chain 'C' and resid 916 through 953 removed outlier: 3.792A pdb=" N ILE C 920 " --> pdb=" O LEU C 916 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 921 " --> pdb=" O GLY C 917 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS C 928 " --> pdb=" O SER C 924 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP C 929 " --> pdb=" O LYS C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 974 removed outlier: 4.825A pdb=" N ARG C 969 " --> pdb=" O ARG C 965 " (cutoff:3.500A) Proline residue: C 970 - end of helix Processing helix chain 'C' and resid 979 through 983 Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.928A pdb=" N VAL C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1050 Processing helix chain 'C' and resid 1053 through 1071 removed outlier: 3.966A pdb=" N SER C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1078 No H-bonds generated for 'chain 'C' and resid 1076 through 1078' Processing helix chain 'C' and resid 1079 through 1088 removed outlier: 4.240A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1142 Processing helix chain 'C' and resid 1143 through 1172 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 98 through 109 removed outlier: 3.799A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 150 removed outlier: 3.843A pdb=" N VAL D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 177 removed outlier: 3.550A pdb=" N ARG D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.540A pdb=" N ILE D 201 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 259 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.798A pdb=" N GLY D 268 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 308 through 317 Processing helix chain 'D' and resid 329 through 337 removed outlier: 3.504A pdb=" N ARG D 337 " --> pdb=" O ASP D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 357 removed outlier: 4.051A pdb=" N GLN D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 384 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 412 Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'D' and resid 425 through 435 Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 503 through 512 Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 571 through 581 removed outlier: 3.556A pdb=" N MET D 581 " --> pdb=" O TYR D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 603 Processing helix chain 'D' and resid 607 through 634 Processing helix chain 'D' and resid 634 through 644 removed outlier: 3.796A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 644 " --> pdb=" O ARG D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 663 through 668 Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.617A pdb=" N PHE D 698 " --> pdb=" O VAL D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 705 Processing helix chain 'D' and resid 767 through 778 Processing helix chain 'D' and resid 778 through 803 Processing helix chain 'D' and resid 811 through 834 Processing helix chain 'D' and resid 852 through 861 Processing helix chain 'D' and resid 862 through 884 Processing helix chain 'D' and resid 887 through 906 Processing helix chain 'D' and resid 907 through 913 Processing helix chain 'D' and resid 916 through 953 removed outlier: 3.792A pdb=" N ILE D 920 " --> pdb=" O LEU D 916 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 921 " --> pdb=" O GLY D 917 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS D 928 " --> pdb=" O SER D 924 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP D 929 " --> pdb=" O LYS D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 974 removed outlier: 4.826A pdb=" N ARG D 969 " --> pdb=" O ARG D 965 " (cutoff:3.500A) Proline residue: D 970 - end of helix Processing helix chain 'D' and resid 979 through 983 Processing helix chain 'D' and resid 1016 through 1033 removed outlier: 3.928A pdb=" N VAL D1020 " --> pdb=" O ALA D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1050 Processing helix chain 'D' and resid 1053 through 1071 removed outlier: 3.965A pdb=" N SER D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1078 No H-bonds generated for 'chain 'D' and resid 1076 through 1078' Processing helix chain 'D' and resid 1079 through 1088 removed outlier: 4.239A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1142 Processing helix chain 'D' and resid 1143 through 1172 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77 removed outlier: 6.480A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 231 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 119 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.139A pdb=" N ASP A 79 " --> pdb=" O TYR A 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 991 removed outlier: 4.304A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP A1000 " --> pdb=" O SER A 991 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 77 removed outlier: 6.479A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP B 236 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 231 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 153 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 119 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.139A pdb=" N ASP B 79 " --> pdb=" O TYR B 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 989 through 991 removed outlier: 4.305A pdb=" N GLU B 989 " --> pdb=" O HIS B1002 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TRP B1000 " --> pdb=" O SER B 991 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 19 Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 77 removed outlier: 6.479A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP C 236 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 231 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE C 153 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C 119 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.139A pdb=" N ASP C 79 " --> pdb=" O TYR C 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 989 through 991 removed outlier: 4.303A pdb=" N GLU C 989 " --> pdb=" O HIS C1002 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP C1000 " --> pdb=" O SER C 991 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 19 Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 77 removed outlier: 6.479A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP D 236 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 231 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE D 153 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL D 119 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.139A pdb=" N ASP D 79 " --> pdb=" O TYR D 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 989 through 991 removed outlier: 4.304A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP D1000 " --> pdb=" O SER D 991 " (cutoff:3.500A) 1892 hydrogen bonds defined for protein. 5496 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: 11.59 Time building geometry restraints manager: 16.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.45: 13164 1.45 - 1.67: 17148 1.67 - 1.89: 296 1.89 - 2.11: 112 2.11 - 2.33: 32 Bond restraints: 30752 Sorted by residual: bond pdb=" CB THR B 823 " pdb=" CG2 THR B 823 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.54e+00 bond pdb=" CB THR C 823 " pdb=" CG2 THR C 823 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.54e+00 bond pdb=" CB THR A 823 " pdb=" CG2 THR A 823 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 bond pdb=" CB THR D 823 " pdb=" CG2 THR D 823 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" CB TRP A 820 " pdb=" CG TRP A 820 " ideal model delta sigma weight residual 1.498 1.468 0.030 3.10e-02 1.04e+03 9.46e-01 ... (remaining 30747 not shown) Histogram of bond angle deviations from ideal: 74.62 - 95.22: 363 95.22 - 115.83: 20134 115.83 - 136.43: 21679 136.43 - 157.04: 64 157.04 - 177.64: 80 Bond angle restraints: 42320 Sorted by residual: angle pdb=" CA TRP C1058 " pdb=" CB TRP C1058 " pdb=" CG TRP C1058 " ideal model delta sigma weight residual 113.60 109.39 4.21 1.90e+00 2.77e-01 4.91e+00 angle pdb=" CA TRP B1058 " pdb=" CB TRP B1058 " pdb=" CG TRP B1058 " ideal model delta sigma weight residual 113.60 109.42 4.18 1.90e+00 2.77e-01 4.84e+00 angle pdb=" CA TRP D1058 " pdb=" CB TRP D1058 " pdb=" CG TRP D1058 " ideal model delta sigma weight residual 113.60 109.43 4.17 1.90e+00 2.77e-01 4.81e+00 angle pdb=" CA TRP A1058 " pdb=" CB TRP A1058 " pdb=" CG TRP A1058 " ideal model delta sigma weight residual 113.60 109.43 4.17 1.90e+00 2.77e-01 4.81e+00 angle pdb=" C PRO C 340 " pdb=" N LYS C 341 " pdb=" CA LYS C 341 " ideal model delta sigma weight residual 121.54 125.59 -4.05 1.91e+00 2.74e-01 4.51e+00 ... (remaining 42315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 16920 15.71 - 31.42: 780 31.42 - 47.13: 204 47.13 - 62.84: 52 62.84 - 78.56: 4 Dihedral angle restraints: 17960 sinusoidal: 6732 harmonic: 11228 Sorted by residual: dihedral pdb=" CA HIS A 447 " pdb=" C HIS A 447 " pdb=" N GLY A 448 " pdb=" CA GLY A 448 " ideal model delta harmonic sigma weight residual 180.00 164.20 15.80 0 5.00e+00 4.00e-02 9.99e+00 dihedral pdb=" CA HIS B 447 " pdb=" C HIS B 447 " pdb=" N GLY B 448 " pdb=" CA GLY B 448 " ideal model delta harmonic sigma weight residual 180.00 164.20 15.80 0 5.00e+00 4.00e-02 9.98e+00 dihedral pdb=" CA HIS C 447 " pdb=" C HIS C 447 " pdb=" N GLY C 448 " pdb=" CA GLY C 448 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.98e+00 ... (remaining 17957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3253 0.029 - 0.058: 1102 0.058 - 0.087: 274 0.087 - 0.116: 118 0.116 - 0.144: 21 Chirality restraints: 4768 Sorted by residual: chirality pdb=" CA ILE D 271 " pdb=" N ILE D 271 " pdb=" C ILE D 271 " pdb=" CB ILE D 271 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE C 271 " pdb=" N ILE C 271 " pdb=" C ILE C 271 " pdb=" CB ILE C 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 4765 not shown) Planarity restraints: 5232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 456 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO D 457 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 457 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 457 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 456 " -0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO B 457 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 457 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 457 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 456 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 457 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " -0.026 5.00e-02 4.00e+02 ... (remaining 5229 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 457 2.68 - 3.23: 30832 3.23 - 3.79: 48222 3.79 - 4.34: 59929 4.34 - 4.90: 103139 Nonbonded interactions: 242579 Sorted by model distance: nonbonded pdb=" OE2 GLU B 828 " pdb="CA CA B2001 " model vdw 2.120 2.510 nonbonded pdb=" OE2 GLU C 828 " pdb="CA CA C2001 " model vdw 2.120 2.510 nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.120 2.510 nonbonded pdb=" OE2 GLU D 828 " pdb="CA CA D2001 " model vdw 2.121 2.510 nonbonded pdb=" NH1 ARG D 195 " pdb=" O PRO D 217 " model vdw 2.209 3.120 ... (remaining 242574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 19.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 86.320 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.130 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30752 Z= 0.289 Angle : 0.475 4.903 42320 Z= 0.261 Chirality : 0.034 0.144 4768 Planarity : 0.003 0.046 5232 Dihedral : 10.411 78.556 10696 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.54 % Allowed : 4.62 % Favored : 94.84 % 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: 2.44 (0.15), residues: 3832 helix: 2.80 (0.11), residues: 2432 sheet: -0.17 (0.39), residues: 200 loop : -0.63 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1058 HIS 0.005 0.001 HIS A1128 PHE 0.013 0.001 PHE B 931 TYR 0.007 0.001 TYR A1063 ARG 0.002 0.000 ARG D 442 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 490 time to evaluate : 3.330 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 254 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7860 (mt-10) REVERT: A 332 ARG cc_start: 0.8967 (ttm110) cc_final: 0.8692 (ttm170) REVERT: A 431 ASP cc_start: 0.8518 (t0) cc_final: 0.8207 (t0) REVERT: A 622 MET cc_start: 0.8020 (mtp) cc_final: 0.7782 (mtp) REVERT: B 254 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7864 (mt-10) REVERT: B 332 ARG cc_start: 0.8937 (ttm110) cc_final: 0.8613 (ttm170) REVERT: B 431 ASP cc_start: 0.8539 (t0) cc_final: 0.8227 (t0) REVERT: C 254 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7843 (mt-10) REVERT: C 332 ARG cc_start: 0.8920 (ttm110) cc_final: 0.8592 (ttm170) REVERT: C 431 ASP cc_start: 0.8526 (t0) cc_final: 0.8211 (t0) REVERT: C 1153 GLN cc_start: 0.9281 (pt0) cc_final: 0.9079 (pp30) REVERT: D 254 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7844 (mt-10) REVERT: D 332 ARG cc_start: 0.8936 (ttm110) cc_final: 0.8614 (ttm170) REVERT: D 431 ASP cc_start: 0.8539 (t0) cc_final: 0.8230 (t0) outliers start: 16 outliers final: 0 residues processed: 502 average time/residue: 0.4222 time to fit residues: 332.4365 Evaluate side-chains 330 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 8.9990 chunk 294 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 304 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 352 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 GLN A1017 ASN B 247 ASN B1014 GLN B1017 ASN C 247 ASN C1014 GLN C1017 ASN D 247 ASN D1014 GLN D1017 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 30752 Z= 0.402 Angle : 0.619 7.499 42320 Z= 0.312 Chirality : 0.040 0.195 4768 Planarity : 0.005 0.047 5232 Dihedral : 3.570 16.255 4284 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.28 % Allowed : 9.51 % Favored : 88.21 % 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: 2.14 (0.14), residues: 3832 helix: 2.47 (0.11), residues: 2452 sheet: 0.15 (0.36), residues: 228 loop : -0.67 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 680 HIS 0.009 0.001 HIS C1128 PHE 0.014 0.001 PHE A 931 TYR 0.016 0.002 TYR A 103 ARG 0.007 0.001 ARG C 857 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 353 time to evaluate : 3.704 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 431 ASP cc_start: 0.8543 (t0) cc_final: 0.8047 (t0) REVERT: A 868 ASP cc_start: 0.8058 (m-30) cc_final: 0.7814 (m-30) REVERT: A 1146 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 431 ASP cc_start: 0.8547 (t0) cc_final: 0.8064 (t0) REVERT: B 670 ASP cc_start: 0.8131 (m-30) cc_final: 0.7821 (m-30) REVERT: B 868 ASP cc_start: 0.8082 (m-30) cc_final: 0.7837 (m-30) REVERT: B 1146 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7752 (tm-30) REVERT: C 431 ASP cc_start: 0.8543 (t0) cc_final: 0.8058 (t0) REVERT: C 868 ASP cc_start: 0.8050 (m-30) cc_final: 0.7809 (m-30) REVERT: C 1146 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7745 (tm-30) REVERT: D 431 ASP cc_start: 0.8548 (t0) cc_final: 0.8065 (t0) REVERT: D 868 ASP cc_start: 0.8082 (m-30) cc_final: 0.7832 (m-30) REVERT: D 1146 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7745 (tm-30) outliers start: 67 outliers final: 35 residues processed: 388 average time/residue: 0.4151 time to fit residues: 263.7576 Evaluate side-chains 339 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 304 time to evaluate : 3.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 930 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 195 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 293 optimal weight: 0.0470 chunk 239 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 352 optimal weight: 7.9990 chunk 381 optimal weight: 0.7980 chunk 314 optimal weight: 6.9990 chunk 350 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30752 Z= 0.253 Angle : 0.552 8.508 42320 Z= 0.277 Chirality : 0.038 0.197 4768 Planarity : 0.004 0.051 5232 Dihedral : 3.574 16.622 4284 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.16 % Allowed : 10.97 % Favored : 85.87 % 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: 2.12 (0.14), residues: 3832 helix: 2.50 (0.11), residues: 2428 sheet: 0.01 (0.36), residues: 232 loop : -0.68 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.008 0.001 HIS D1128 PHE 0.010 0.001 PHE C 931 TYR 0.012 0.001 TYR C 971 ARG 0.004 0.000 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 364 time to evaluate : 3.841 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 431 ASP cc_start: 0.8363 (t0) cc_final: 0.7858 (t0) REVERT: A 868 ASP cc_start: 0.8082 (m-30) cc_final: 0.7784 (m-30) REVERT: A 941 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9118 (mp) REVERT: A 1146 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 431 ASP cc_start: 0.8389 (t0) cc_final: 0.7909 (t0) REVERT: B 868 ASP cc_start: 0.8095 (m-30) cc_final: 0.7821 (m-30) REVERT: B 941 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9121 (mp) REVERT: B 1146 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 1149 LYS cc_start: 0.9018 (tppt) cc_final: 0.7756 (tppt) REVERT: C 431 ASP cc_start: 0.8383 (t0) cc_final: 0.7909 (t0) REVERT: C 868 ASP cc_start: 0.8088 (m-30) cc_final: 0.7819 (m-30) REVERT: C 941 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9126 (mp) REVERT: C 1146 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7745 (tm-30) REVERT: C 1149 LYS cc_start: 0.9012 (tppt) cc_final: 0.8732 (tppt) REVERT: D 431 ASP cc_start: 0.8387 (t0) cc_final: 0.7908 (t0) REVERT: D 868 ASP cc_start: 0.8090 (m-30) cc_final: 0.7816 (m-30) REVERT: D 941 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9132 (mp) REVERT: D 1146 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7742 (tm-30) outliers start: 93 outliers final: 63 residues processed: 421 average time/residue: 0.3810 time to fit residues: 265.5450 Evaluate side-chains 395 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 328 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 348 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 168 optimal weight: 0.7980 chunk 237 optimal weight: 9.9990 chunk 354 optimal weight: 0.7980 chunk 375 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 335 optimal weight: 9.9990 chunk 101 optimal weight: 30.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30752 Z= 0.236 Angle : 0.534 8.335 42320 Z= 0.269 Chirality : 0.038 0.210 4768 Planarity : 0.004 0.051 5232 Dihedral : 3.570 21.215 4284 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.50 % Allowed : 11.68 % Favored : 84.82 % 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: 2.13 (0.14), residues: 3832 helix: 2.54 (0.11), residues: 2424 sheet: -0.45 (0.33), residues: 260 loop : -0.64 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.007 0.001 HIS A1128 PHE 0.011 0.001 PHE B 902 TYR 0.012 0.001 TYR A1063 ARG 0.006 0.000 ARG B1136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 341 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 431 ASP cc_start: 0.8398 (t0) cc_final: 0.7853 (t0) REVERT: A 868 ASP cc_start: 0.8074 (m-30) cc_final: 0.7788 (m-30) REVERT: A 941 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9122 (mp) REVERT: A 1134 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9178 (tt) REVERT: A 1146 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 431 ASP cc_start: 0.8424 (t0) cc_final: 0.7855 (t0) REVERT: B 868 ASP cc_start: 0.8075 (m-30) cc_final: 0.7792 (m-30) REVERT: B 941 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9128 (mp) REVERT: B 1134 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9163 (tt) REVERT: B 1146 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7764 (tm-30) REVERT: C 431 ASP cc_start: 0.8427 (t0) cc_final: 0.7866 (t0) REVERT: C 868 ASP cc_start: 0.8072 (m-30) cc_final: 0.7791 (m-30) REVERT: C 941 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9126 (mp) REVERT: C 1134 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9173 (tt) REVERT: C 1146 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7802 (tm-30) REVERT: D 431 ASP cc_start: 0.8423 (t0) cc_final: 0.7854 (t0) REVERT: D 868 ASP cc_start: 0.8067 (m-30) cc_final: 0.7784 (m-30) REVERT: D 941 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9127 (mp) REVERT: D 1134 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9154 (tt) REVERT: D 1146 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7820 (tm-30) outliers start: 103 outliers final: 72 residues processed: 409 average time/residue: 0.3713 time to fit residues: 251.8555 Evaluate side-chains 401 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 321 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1134 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 781 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 934 LEU Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1134 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 312 optimal weight: 0.5980 chunk 212 optimal weight: 0.1980 chunk 5 optimal weight: 30.0000 chunk 279 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 320 optimal weight: 20.0000 chunk 259 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 191 optimal weight: 0.5980 chunk 336 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 30752 Z= 0.144 Angle : 0.506 9.142 42320 Z= 0.253 Chirality : 0.037 0.256 4768 Planarity : 0.004 0.048 5232 Dihedral : 3.487 19.874 4284 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.23 % Allowed : 12.43 % Favored : 84.34 % 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: 2.16 (0.14), residues: 3832 helix: 2.56 (0.11), residues: 2444 sheet: -0.28 (0.35), residues: 236 loop : -0.73 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.005 0.001 HIS A1128 PHE 0.012 0.001 PHE A 902 TYR 0.012 0.001 TYR B1063 ARG 0.007 0.000 ARG C1136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 392 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 86 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7538 (tppt) REVERT: A 431 ASP cc_start: 0.8260 (t0) cc_final: 0.7648 (t0) REVERT: A 868 ASP cc_start: 0.8100 (m-30) cc_final: 0.7759 (m-30) REVERT: A 941 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9115 (mp) REVERT: A 1134 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9166 (tt) REVERT: A 1146 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 1149 LYS cc_start: 0.8976 (tppt) cc_final: 0.8204 (tppt) REVERT: B 86 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7566 (tppt) REVERT: B 431 ASP cc_start: 0.8285 (t0) cc_final: 0.7694 (t0) REVERT: B 868 ASP cc_start: 0.8101 (m-30) cc_final: 0.7764 (m-30) REVERT: B 941 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9113 (mp) REVERT: B 1134 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9151 (tt) REVERT: B 1146 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7791 (tm-30) REVERT: C 431 ASP cc_start: 0.8288 (t0) cc_final: 0.7705 (t0) REVERT: C 868 ASP cc_start: 0.8102 (m-30) cc_final: 0.7769 (m-30) REVERT: C 941 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9118 (mp) REVERT: C 1134 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9175 (tt) REVERT: C 1146 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7830 (tm-30) REVERT: D 431 ASP cc_start: 0.8300 (t0) cc_final: 0.7701 (t0) REVERT: D 868 ASP cc_start: 0.8099 (m-30) cc_final: 0.7763 (m-30) REVERT: D 941 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9115 (mp) REVERT: D 1134 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9151 (tt) REVERT: D 1146 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7833 (tm-30) outliers start: 95 outliers final: 60 residues processed: 455 average time/residue: 0.3851 time to fit residues: 288.5194 Evaluate side-chains 429 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 359 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1134 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1134 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 126 optimal weight: 8.9990 chunk 337 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 375 optimal weight: 1.9990 chunk 311 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 197 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1032 ASN B 350 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 GLN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 30752 Z= 0.509 Angle : 0.642 7.327 42320 Z= 0.324 Chirality : 0.041 0.228 4768 Planarity : 0.005 0.047 5232 Dihedral : 3.624 22.245 4284 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.40 % Allowed : 12.74 % Favored : 83.87 % 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: 2.01 (0.14), residues: 3832 helix: 2.46 (0.11), residues: 2428 sheet: -0.55 (0.34), residues: 236 loop : -0.74 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1124 HIS 0.008 0.001 HIS A1128 PHE 0.015 0.002 PHE A 931 TYR 0.012 0.001 TYR B 464 ARG 0.006 0.001 ARG C1136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 325 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 86 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7624 (tppt) REVERT: A 431 ASP cc_start: 0.8371 (t0) cc_final: 0.7820 (t0) REVERT: A 644 ARG cc_start: 0.5698 (tpt170) cc_final: 0.2755 (ttp80) REVERT: A 868 ASP cc_start: 0.8157 (m-30) cc_final: 0.7543 (m-30) REVERT: A 941 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9133 (mp) REVERT: A 1134 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9203 (tt) REVERT: A 1146 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7742 (tm-30) REVERT: B 86 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7616 (tppt) REVERT: B 431 ASP cc_start: 0.8400 (t0) cc_final: 0.7844 (t0) REVERT: B 644 ARG cc_start: 0.5651 (tpt170) cc_final: 0.2724 (ttp80) REVERT: B 868 ASP cc_start: 0.8158 (m-30) cc_final: 0.7542 (m-30) REVERT: B 941 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9131 (mp) REVERT: B 1134 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9184 (tt) REVERT: B 1146 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7780 (tm-30) REVERT: C 431 ASP cc_start: 0.8486 (t0) cc_final: 0.7930 (t0) REVERT: C 644 ARG cc_start: 0.5652 (tpt170) cc_final: 0.2726 (ttp80) REVERT: C 868 ASP cc_start: 0.8154 (m-30) cc_final: 0.7542 (m-30) REVERT: C 941 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9135 (mp) REVERT: C 1134 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9173 (tt) REVERT: C 1146 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7760 (tm-30) REVERT: D 431 ASP cc_start: 0.8397 (t0) cc_final: 0.7840 (t0) REVERT: D 644 ARG cc_start: 0.5654 (tpt170) cc_final: 0.2728 (ttp80) REVERT: D 868 ASP cc_start: 0.8151 (m-30) cc_final: 0.7532 (m-30) REVERT: D 941 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9122 (mp) REVERT: D 1134 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9154 (tt) REVERT: D 1146 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7839 (tm-30) outliers start: 100 outliers final: 65 residues processed: 388 average time/residue: 0.3889 time to fit residues: 248.2377 Evaluate side-chains 390 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 315 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1134 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 934 LEU Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1134 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 361 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 213 optimal weight: 7.9990 chunk 274 optimal weight: 0.9980 chunk 212 optimal weight: 20.0000 chunk 316 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 373 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 227 optimal weight: 0.5980 chunk 172 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30752 Z= 0.168 Angle : 0.543 9.133 42320 Z= 0.269 Chirality : 0.037 0.239 4768 Planarity : 0.004 0.047 5232 Dihedral : 3.552 20.109 4284 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.62 % Allowed : 14.74 % Favored : 82.64 % 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: 2.09 (0.14), residues: 3832 helix: 2.46 (0.11), residues: 2452 sheet: -0.39 (0.35), residues: 236 loop : -0.64 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1058 HIS 0.006 0.001 HIS A1128 PHE 0.010 0.001 PHE B 627 TYR 0.013 0.001 TYR A1063 ARG 0.012 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 359 time to evaluate : 3.255 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7549 (tppt) REVERT: A 430 MET cc_start: 0.8840 (tpp) cc_final: 0.8589 (tpp) REVERT: A 431 ASP cc_start: 0.8301 (t0) cc_final: 0.7691 (t0) REVERT: A 644 ARG cc_start: 0.5683 (tpt170) cc_final: 0.2536 (tmm160) REVERT: A 868 ASP cc_start: 0.8112 (m-30) cc_final: 0.7522 (m-30) REVERT: A 941 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9102 (mp) REVERT: A 1134 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9167 (tt) REVERT: A 1146 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7760 (tm-30) REVERT: B 86 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7545 (tppt) REVERT: B 430 MET cc_start: 0.8842 (tpp) cc_final: 0.8594 (tpp) REVERT: B 431 ASP cc_start: 0.8291 (t0) cc_final: 0.7681 (t0) REVERT: B 644 ARG cc_start: 0.5629 (tpt170) cc_final: 0.2480 (tmm160) REVERT: B 868 ASP cc_start: 0.8113 (m-30) cc_final: 0.7523 (m-30) REVERT: B 941 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9097 (mp) REVERT: B 1134 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9150 (tt) REVERT: B 1146 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7831 (tm-30) REVERT: C 431 ASP cc_start: 0.8327 (t0) cc_final: 0.7706 (t0) REVERT: C 644 ARG cc_start: 0.5629 (tpt170) cc_final: 0.2482 (tmm160) REVERT: C 868 ASP cc_start: 0.8112 (m-30) cc_final: 0.7526 (m-30) REVERT: C 941 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9102 (mp) REVERT: C 1134 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9147 (tt) REVERT: C 1146 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7775 (tm-30) REVERT: D 430 MET cc_start: 0.8843 (tpp) cc_final: 0.8595 (tpp) REVERT: D 431 ASP cc_start: 0.8295 (t0) cc_final: 0.7685 (t0) REVERT: D 644 ARG cc_start: 0.5632 (tpt170) cc_final: 0.2479 (tmm160) REVERT: D 868 ASP cc_start: 0.8111 (m-30) cc_final: 0.7517 (m-30) REVERT: D 941 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9110 (mp) REVERT: D 1146 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7795 (tm-30) outliers start: 77 outliers final: 63 residues processed: 404 average time/residue: 0.3824 time to fit residues: 255.1689 Evaluate side-chains 410 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 338 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain C residue 1134 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 981 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 231 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 chunk 72 optimal weight: 0.0470 chunk 237 optimal weight: 9.9990 chunk 254 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 293 optimal weight: 0.0670 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 GLN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30752 Z= 0.149 Angle : 0.521 8.317 42320 Z= 0.259 Chirality : 0.036 0.196 4768 Planarity : 0.004 0.047 5232 Dihedral : 3.477 19.926 4284 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.62 % Allowed : 14.47 % Favored : 82.91 % 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: 2.18 (0.14), residues: 3832 helix: 2.54 (0.11), residues: 2448 sheet: -0.32 (0.35), residues: 236 loop : -0.63 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1058 HIS 0.004 0.001 HIS A1128 PHE 0.012 0.001 PHE D 627 TYR 0.010 0.001 TYR A1063 ARG 0.011 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 378 time to evaluate : 3.562 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7538 (tppt) REVERT: A 430 MET cc_start: 0.8776 (tpp) cc_final: 0.8559 (tpp) REVERT: A 431 ASP cc_start: 0.8283 (t0) cc_final: 0.7694 (t0) REVERT: A 644 ARG cc_start: 0.5568 (tpt170) cc_final: 0.3303 (mmm-85) REVERT: A 868 ASP cc_start: 0.8073 (m-30) cc_final: 0.7452 (m-30) REVERT: A 941 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9119 (mp) REVERT: A 1068 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8273 (tm-30) REVERT: A 1134 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9168 (tt) REVERT: A 1146 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 86 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7550 (tppt) REVERT: B 430 MET cc_start: 0.8815 (tpp) cc_final: 0.8580 (tpp) REVERT: B 431 ASP cc_start: 0.8293 (t0) cc_final: 0.7707 (t0) REVERT: B 644 ARG cc_start: 0.5517 (tpt170) cc_final: 0.3261 (mmm-85) REVERT: B 868 ASP cc_start: 0.8081 (m-30) cc_final: 0.7460 (m-30) REVERT: B 941 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9110 (mp) REVERT: B 1068 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8272 (tm-30) REVERT: B 1134 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9161 (tt) REVERT: B 1140 LYS cc_start: 0.9280 (tmtt) cc_final: 0.9047 (tmtt) REVERT: B 1146 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7718 (tm-30) REVERT: C 431 ASP cc_start: 0.8270 (t0) cc_final: 0.7717 (t0) REVERT: C 868 ASP cc_start: 0.8072 (m-30) cc_final: 0.7456 (m-30) REVERT: C 941 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9113 (mp) REVERT: C 1068 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8277 (tm-30) REVERT: C 1134 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9176 (tt) REVERT: C 1140 LYS cc_start: 0.9267 (tmtt) cc_final: 0.9035 (tmtt) REVERT: C 1146 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7705 (tm-30) REVERT: D 430 MET cc_start: 0.8815 (tpp) cc_final: 0.8581 (tpp) REVERT: D 431 ASP cc_start: 0.8293 (t0) cc_final: 0.7707 (t0) REVERT: D 644 ARG cc_start: 0.5518 (tpt170) cc_final: 0.3262 (mmm-85) REVERT: D 868 ASP cc_start: 0.8070 (m-30) cc_final: 0.7445 (m-30) REVERT: D 941 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9122 (mp) REVERT: D 1068 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8277 (tm-30) REVERT: D 1140 LYS cc_start: 0.9271 (tmtt) cc_final: 0.9022 (tmtt) REVERT: D 1146 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7734 (tm-30) outliers start: 77 outliers final: 64 residues processed: 425 average time/residue: 0.3747 time to fit residues: 264.4219 Evaluate side-chains 434 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 361 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain C residue 1134 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 981 GLU Chi-restraints excluded: chain D residue 1134 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 340 optimal weight: 5.9990 chunk 358 optimal weight: 4.9990 chunk 326 optimal weight: 0.7980 chunk 348 optimal weight: 4.9990 chunk 209 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 273 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 314 optimal weight: 7.9990 chunk 329 optimal weight: 0.9980 chunk 347 optimal weight: 2.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30752 Z= 0.243 Angle : 0.540 11.314 42320 Z= 0.268 Chirality : 0.037 0.231 4768 Planarity : 0.004 0.046 5232 Dihedral : 3.447 20.132 4284 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.89 % Allowed : 14.03 % Favored : 83.08 % 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: 2.16 (0.14), residues: 3832 helix: 2.53 (0.11), residues: 2448 sheet: -0.41 (0.35), residues: 236 loop : -0.62 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1124 HIS 0.005 0.001 HIS D1128 PHE 0.012 0.001 PHE D 627 TYR 0.010 0.001 TYR A1063 ARG 0.008 0.000 ARG C1136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 347 time to evaluate : 3.318 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 86 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7574 (tppt) REVERT: A 430 MET cc_start: 0.8790 (tpp) cc_final: 0.8573 (tpp) REVERT: A 431 ASP cc_start: 0.8351 (t0) cc_final: 0.7784 (t0) REVERT: A 644 ARG cc_start: 0.5671 (tpt170) cc_final: 0.3428 (mmm-85) REVERT: A 868 ASP cc_start: 0.8125 (m-30) cc_final: 0.7553 (m-30) REVERT: A 941 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9125 (mp) REVERT: A 1134 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9171 (tt) REVERT: A 1146 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7803 (tm-30) REVERT: B 86 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7571 (tppt) REVERT: B 430 MET cc_start: 0.8807 (tpp) cc_final: 0.8562 (tpp) REVERT: B 431 ASP cc_start: 0.8350 (t0) cc_final: 0.7811 (t0) REVERT: B 644 ARG cc_start: 0.5682 (tpt170) cc_final: 0.2668 (ttp80) REVERT: B 868 ASP cc_start: 0.8125 (m-30) cc_final: 0.7546 (m-30) REVERT: B 941 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9119 (mp) REVERT: B 1134 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9178 (tt) REVERT: B 1146 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7774 (tm-30) REVERT: C 431 ASP cc_start: 0.8370 (t0) cc_final: 0.7812 (t0) REVERT: C 644 ARG cc_start: 0.5685 (tpt170) cc_final: 0.2672 (ttp80) REVERT: C 868 ASP cc_start: 0.8157 (m-30) cc_final: 0.7574 (m-30) REVERT: C 941 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9119 (mp) REVERT: C 1134 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9174 (tt) REVERT: C 1146 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7722 (tm-30) REVERT: D 430 MET cc_start: 0.8806 (tpp) cc_final: 0.8563 (tpp) REVERT: D 431 ASP cc_start: 0.8347 (t0) cc_final: 0.7810 (t0) REVERT: D 644 ARG cc_start: 0.5684 (tpt170) cc_final: 0.2510 (tmm160) REVERT: D 868 ASP cc_start: 0.8157 (m-30) cc_final: 0.7567 (m-30) REVERT: D 941 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9113 (mp) REVERT: D 1146 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7834 (tm-30) outliers start: 85 outliers final: 70 residues processed: 397 average time/residue: 0.3750 time to fit residues: 248.1370 Evaluate side-chains 414 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 335 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain C residue 1134 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 981 GLU Chi-restraints excluded: chain D residue 1134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 228 optimal weight: 0.5980 chunk 368 optimal weight: 3.9990 chunk 224 optimal weight: 0.0470 chunk 174 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 386 optimal weight: 6.9990 chunk 355 optimal weight: 2.9990 chunk 307 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 188 optimal weight: 0.9980 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30752 Z= 0.202 Angle : 0.544 8.899 42320 Z= 0.271 Chirality : 0.037 0.223 4768 Planarity : 0.004 0.048 5232 Dihedral : 3.445 19.833 4284 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.72 % Allowed : 14.40 % Favored : 82.88 % 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: 2.15 (0.14), residues: 3832 helix: 2.51 (0.11), residues: 2448 sheet: -0.41 (0.35), residues: 236 loop : -0.60 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1058 HIS 0.005 0.001 HIS A1128 PHE 0.013 0.001 PHE D 627 TYR 0.011 0.001 TYR B1063 ARG 0.013 0.000 ARG A 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 349 time to evaluate : 3.306 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7589 (tppt) REVERT: A 431 ASP cc_start: 0.8320 (t0) cc_final: 0.7754 (t0) REVERT: A 644 ARG cc_start: 0.5568 (tpt170) cc_final: 0.2423 (tmm160) REVERT: A 868 ASP cc_start: 0.8107 (m-30) cc_final: 0.7535 (m-30) REVERT: A 941 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9113 (mp) REVERT: A 1134 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9166 (tt) REVERT: A 1146 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7816 (tm-30) REVERT: B 86 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7576 (tppt) REVERT: B 431 ASP cc_start: 0.8322 (t0) cc_final: 0.7758 (t0) REVERT: B 644 ARG cc_start: 0.5557 (tpt170) cc_final: 0.2414 (tmm160) REVERT: B 868 ASP cc_start: 0.8104 (m-30) cc_final: 0.7530 (m-30) REVERT: B 941 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9136 (mp) REVERT: B 1134 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9171 (tt) REVERT: B 1146 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7760 (tm-30) REVERT: C 431 ASP cc_start: 0.8331 (t0) cc_final: 0.7767 (t0) REVERT: C 644 ARG cc_start: 0.5685 (tpt170) cc_final: 0.2497 (tmm160) REVERT: C 868 ASP cc_start: 0.8105 (m-30) cc_final: 0.7532 (m-30) REVERT: C 941 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9137 (mp) REVERT: C 1134 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9170 (tt) REVERT: C 1146 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7760 (tm-30) REVERT: D 431 ASP cc_start: 0.8323 (t0) cc_final: 0.7758 (t0) REVERT: D 644 ARG cc_start: 0.5563 (tpt170) cc_final: 0.2417 (tmm160) REVERT: D 868 ASP cc_start: 0.8106 (m-30) cc_final: 0.7527 (m-30) REVERT: D 941 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9128 (mp) REVERT: D 1146 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7813 (tm-30) outliers start: 80 outliers final: 67 residues processed: 396 average time/residue: 0.3723 time to fit residues: 245.1450 Evaluate side-chains 422 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 346 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain C residue 1134 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 981 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 9.9990 chunk 327 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 283 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 308 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.102534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.071265 restraints weight = 78765.553| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.28 r_work: 0.2844 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30752 Z= 0.235 Angle : 0.555 9.477 42320 Z= 0.275 Chirality : 0.037 0.212 4768 Planarity : 0.004 0.046 5232 Dihedral : 3.444 19.901 4284 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.72 % Allowed : 14.50 % Favored : 82.78 % 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: 2.15 (0.14), residues: 3832 helix: 2.50 (0.11), residues: 2448 sheet: -0.43 (0.35), residues: 236 loop : -0.58 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1058 HIS 0.006 0.001 HIS D1128 PHE 0.013 0.001 PHE D 627 TYR 0.011 0.001 TYR B1063 ARG 0.008 0.000 ARG B1136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7104.49 seconds wall clock time: 127 minutes 59.66 seconds (7679.66 seconds total)