Starting phenix.real_space_refine on Sun Jun 29 14:51:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g2j_29679/06_2025/8g2j_29679_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g2j_29679/06_2025/8g2j_29679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g2j_29679/06_2025/8g2j_29679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g2j_29679/06_2025/8g2j_29679.map" model { file = "/net/cci-nas-00/data/ceres_data/8g2j_29679/06_2025/8g2j_29679_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g2j_29679/06_2025/8g2j_29679_trim.cif" } resolution = 3.3 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= 0.003 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 87 5.16 5 C 11437 2.51 5 N 2884 2.21 5 O 3132 1.98 5 H 16852 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34401 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 11356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 11356 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 673} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 11394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11394 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 675} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 11372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 11372 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 674} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' MG': 1, 'UPG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' MG': 1, 'UPG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' MG': 1, 'UPG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.66, per 1000 atoms: 0.46 Number of scatterers: 34401 At special positions: 0 Unit cell: (133.65, 130.35, 102.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 87 16.00 P 6 15.00 Mg 3 11.99 O 3132 8.00 N 2884 7.00 C 11437 6.00 H 16852 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " BGC A 1 " - " BGC A 2 " " BGC A 2 " - " BGC A 3 " " BGC A 3 " - " BGC A 4 " " BGC A 4 " - " BGC A 5 " " BGC B 1 " - " BGC B 2 " " BGC B 2 " - " BGC B 3 " " BGC B 3 " - " BGC B 4 " " BGC B 4 " - " BGC B 5 " " BGC E 1 " - " BGC E 2 " " BGC E 2 " - " BGC E 3 " " BGC E 3 " - " BGC E 4 " " BGC E 4 " - " BGC E 5 " Time building additional restraints: 9.41 Conformation dependent library (CDL) restraints added in 2.9 seconds 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 11 sheets defined 57.9% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'D' and resid 170 through 194 removed outlier: 3.733A pdb=" N ILE D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN D 194 " --> pdb=" O TYR D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 222 removed outlier: 3.557A pdb=" N PHE D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 233 through 242 removed outlier: 4.174A pdb=" N LEU D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 279 removed outlier: 3.815A pdb=" N THR D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 322 removed outlier: 3.562A pdb=" N ARG D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Proline residue: D 316 - end of helix Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.591A pdb=" N SER D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 372 Processing helix chain 'D' and resid 436 through 452 Processing helix chain 'D' and resid 469 through 479 removed outlier: 4.068A pdb=" N ILE D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 515 removed outlier: 3.675A pdb=" N PHE D 513 " --> pdb=" O ASN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 521 Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 611 through 618 Processing helix chain 'D' and resid 621 through 628 Processing helix chain 'D' and resid 640 through 651 Processing helix chain 'D' and resid 674 through 686 removed outlier: 3.715A pdb=" N LEU D 678 " --> pdb=" O THR D 674 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG D 686 " --> pdb=" O LYS D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 728 Processing helix chain 'D' and resid 743 through 756 removed outlier: 3.692A pdb=" N LEU D 748 " --> pdb=" O TRP D 744 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA D 749 " --> pdb=" O LEU D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 776 Proline residue: D 770 - end of helix Processing helix chain 'D' and resid 787 through 811 removed outlier: 3.596A pdb=" N LEU D 791 " --> pdb=" O LEU D 787 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 800 " --> pdb=" O PHE D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 846 removed outlier: 3.929A pdb=" N ILE D 826 " --> pdb=" O GLN D 822 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS D 832 " --> pdb=" O GLY D 828 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU D 833 " --> pdb=" O VAL D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 875 removed outlier: 3.518A pdb=" N LEU D 875 " --> pdb=" O TRP D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 899 removed outlier: 3.504A pdb=" N PHE D 893 " --> pdb=" O VAL D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 928 Proline residue: D 923 - end of helix Processing helix chain 'D' and resid 939 through 954 removed outlier: 3.811A pdb=" N SER D 943 " --> pdb=" O VAL D 939 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 193 removed outlier: 3.617A pdb=" N ILE I 182 " --> pdb=" O ILE I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 222 Processing helix chain 'I' and resid 223 through 225 No H-bonds generated for 'chain 'I' and resid 223 through 225' Processing helix chain 'I' and resid 233 through 241 removed outlier: 4.004A pdb=" N LEU I 237 " --> pdb=" O PHE I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 279 removed outlier: 3.802A pdb=" N THR I 270 " --> pdb=" O PRO I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 322 removed outlier: 3.557A pdb=" N ARG I 312 " --> pdb=" O ALA I 308 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS I 313 " --> pdb=" O GLU I 309 " (cutoff:3.500A) Proline residue: I 316 - end of helix Processing helix chain 'I' and resid 327 through 333 removed outlier: 3.607A pdb=" N SER I 333 " --> pdb=" O GLU I 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 372 Processing helix chain 'I' and resid 436 through 452 removed outlier: 3.523A pdb=" N ASN I 452 " --> pdb=" O ALA I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 479 removed outlier: 4.188A pdb=" N ILE I 477 " --> pdb=" O GLU I 473 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU I 478 " --> pdb=" O ALA I 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 482 through 486 removed outlier: 4.139A pdb=" N ASP I 486 " --> pdb=" O VAL I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 515 removed outlier: 3.526A pdb=" N PHE I 513 " --> pdb=" O ASN I 509 " (cutoff:3.500A) Processing helix chain 'I' and resid 515 through 521 Processing helix chain 'I' and resid 537 through 542 Processing helix chain 'I' and resid 611 through 619 Processing helix chain 'I' and resid 621 through 628 Processing helix chain 'I' and resid 640 through 651 Processing helix chain 'I' and resid 674 through 686 removed outlier: 3.608A pdb=" N LEU I 678 " --> pdb=" O THR I 674 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET I 683 " --> pdb=" O SER I 679 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG I 686 " --> pdb=" O LYS I 682 " (cutoff:3.500A) Processing helix chain 'I' and resid 707 through 728 Processing helix chain 'I' and resid 743 through 756 removed outlier: 3.919A pdb=" N LEU I 748 " --> pdb=" O TRP I 744 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA I 749 " --> pdb=" O LEU I 745 " (cutoff:3.500A) Processing helix chain 'I' and resid 759 through 776 Proline residue: I 770 - end of helix Processing helix chain 'I' and resid 787 through 811 Processing helix chain 'I' and resid 813 through 830 removed outlier: 3.519A pdb=" N VAL I 825 " --> pdb=" O GLU I 821 " (cutoff:3.500A) Processing helix chain 'I' and resid 830 through 846 Processing helix chain 'I' and resid 870 through 875 removed outlier: 3.846A pdb=" N LEU I 875 " --> pdb=" O TRP I 871 " (cutoff:3.500A) Processing helix chain 'I' and resid 875 through 899 Processing helix chain 'I' and resid 905 through 927 Proline residue: I 923 - end of helix Processing helix chain 'I' and resid 928 through 930 No H-bonds generated for 'chain 'I' and resid 928 through 930' Processing helix chain 'I' and resid 938 through 956 removed outlier: 4.337A pdb=" N TRP I 942 " --> pdb=" O ILE I 938 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER I 943 " --> pdb=" O VAL I 939 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER I 948 " --> pdb=" O VAL I 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 194 removed outlier: 3.532A pdb=" N ILE C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN C 194 " --> pdb=" O TYR C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 222 removed outlier: 3.623A pdb=" N PHE C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.762A pdb=" N LEU C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 279 removed outlier: 4.030A pdb=" N THR C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 322 removed outlier: 3.718A pdb=" N ARG C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Proline residue: C 316 - end of helix Processing helix chain 'C' and resid 327 through 333 removed outlier: 3.648A pdb=" N SER C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 372 removed outlier: 3.610A pdb=" N ALA C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 451 Processing helix chain 'C' and resid 469 through 479 removed outlier: 3.998A pdb=" N ILE C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 4.171A pdb=" N ASP C 486 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 515 removed outlier: 3.938A pdb=" N PHE C 513 " --> pdb=" O ASN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 522 removed outlier: 3.768A pdb=" N GLY C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 621 through 628 Processing helix chain 'C' and resid 640 through 651 Processing helix chain 'C' and resid 674 through 686 removed outlier: 3.885A pdb=" N LEU C 678 " --> pdb=" O THR C 674 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG C 686 " --> pdb=" O LYS C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 728 Processing helix chain 'C' and resid 743 through 756 removed outlier: 3.885A pdb=" N LEU C 748 " --> pdb=" O TRP C 744 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA C 749 " --> pdb=" O LEU C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 776 Proline residue: C 770 - end of helix Processing helix chain 'C' and resid 787 through 811 removed outlier: 3.629A pdb=" N LEU C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 830 removed outlier: 3.739A pdb=" N ILE C 826 " --> pdb=" O GLN C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 846 Processing helix chain 'C' and resid 870 through 875 Processing helix chain 'C' and resid 875 through 899 removed outlier: 3.521A pdb=" N THR C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 922 removed outlier: 3.521A pdb=" N HIS C 920 " --> pdb=" O TRP C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 928 Processing helix chain 'C' and resid 934 through 953 removed outlier: 5.329A pdb=" N VAL C 940 " --> pdb=" O PRO C 936 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 160 through 164 Processing sheet with id=AA2, first strand: chain 'D' and resid 399 through 403 removed outlier: 4.413A pdb=" N ARG D 419 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP D 293 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL D 253 " --> pdb=" O SER D 288 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N TYR D 290 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE D 255 " --> pdb=" O TYR D 290 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N SER D 292 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL D 257 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP D 254 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU D 459 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N PHE D 256 " --> pdb=" O LEU D 459 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS D 533 " --> pdb=" O ASN D 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AA4, first strand: chain 'D' and resid 495 through 496 removed outlier: 7.056A pdb=" N ARG D 495 " --> pdb=" O GLY D 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'I' and resid 160 through 164 Processing sheet with id=AA6, first strand: chain 'I' and resid 399 through 403 removed outlier: 4.451A pdb=" N ARG I 419 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP I 293 " --> pdb=" O VAL I 423 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP I 254 " --> pdb=" O LEU I 457 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU I 459 " --> pdb=" O ASP I 254 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE I 256 " --> pdb=" O LEU I 459 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS I 533 " --> pdb=" O ASN I 458 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 489 through 491 Processing sheet with id=AA8, first strand: chain 'I' and resid 495 through 497 removed outlier: 6.678A pdb=" N ARG I 495 " --> pdb=" O GLY I 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 160 through 164 Processing sheet with id=AB1, first strand: chain 'C' and resid 399 through 403 removed outlier: 3.753A pdb=" N ASP C 293 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP C 254 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU C 459 " --> pdb=" O ASP C 254 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N PHE C 256 " --> pdb=" O LEU C 459 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N CYS C 533 " --> pdb=" O ASN C 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 495 through 496 removed outlier: 7.004A pdb=" N ARG C 495 " --> pdb=" O GLY C 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 901 hydrogen bonds defined for protein. 2685 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: 11.76 Time building geometry restraints manager: 10.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16813 1.03 - 1.23: 45 1.23 - 1.42: 7623 1.42 - 1.61: 10277 1.61 - 1.81: 150 Bond restraints: 34908 Sorted by residual: bond pdb=" C2C UPG D1001 " pdb=" C3C UPG D1001 " ideal model delta sigma weight residual 1.531 1.328 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C2C UPG C1001 " pdb=" C3C UPG C1001 " ideal model delta sigma weight residual 1.531 1.329 0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C1C UPG D1001 " pdb=" O4C UPG D1001 " ideal model delta sigma weight residual 1.399 1.584 -0.185 2.00e-02 2.50e+03 8.52e+01 bond pdb=" C2C UPG I1001 " pdb=" C3C UPG I1001 " ideal model delta sigma weight residual 1.531 1.348 0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" C1C UPG C1001 " pdb=" O4C UPG C1001 " ideal model delta sigma weight residual 1.399 1.580 -0.181 2.00e-02 2.50e+03 8.16e+01 ... (remaining 34903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.45: 62741 7.45 - 14.90: 23 14.90 - 22.35: 6 22.35 - 29.80: 22 29.80 - 37.25: 61 Bond angle restraints: 62853 Sorted by residual: angle pdb=" C3C UPG I1001 " pdb=" C2C UPG I1001 " pdb=" O2C UPG I1001 " ideal model delta sigma weight residual 116.50 79.25 37.25 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C ALA D 639 " pdb=" CA ALA D 639 " pdb=" HA ALA D 639 " ideal model delta sigma weight residual 109.00 72.99 36.01 3.00e+00 1.11e-01 1.44e+02 angle pdb=" C ALA I 639 " pdb=" CA ALA I 639 " pdb=" HA ALA I 639 " ideal model delta sigma weight residual 109.00 73.07 35.93 3.00e+00 1.11e-01 1.43e+02 angle pdb=" C ALA C 639 " pdb=" CA ALA C 639 " pdb=" HA ALA C 639 " ideal model delta sigma weight residual 109.00 73.11 35.89 3.00e+00 1.11e-01 1.43e+02 angle pdb=" C THR I 937 " pdb=" CA THR I 937 " pdb=" HA THR I 937 " ideal model delta sigma weight residual 109.00 73.16 35.84 3.00e+00 1.11e-01 1.43e+02 ... (remaining 62848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 16164 25.94 - 51.89: 547 51.89 - 77.83: 144 77.83 - 103.78: 16 103.78 - 129.72: 15 Dihedral angle restraints: 16886 sinusoidal: 9188 harmonic: 7698 Sorted by residual: dihedral pdb=" CA GLY I 905 " pdb=" C GLY I 905 " pdb=" N PRO I 906 " pdb=" CA PRO I 906 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA GLY C 905 " pdb=" C GLY C 905 " pdb=" N PRO C 906 " pdb=" CA PRO C 906 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLY D 905 " pdb=" C GLY D 905 " pdb=" N PRO D 906 " pdb=" CA PRO D 906 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 16883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.289: 2720 0.289 - 0.578: 21 0.578 - 0.866: 0 0.866 - 1.155: 0 1.155 - 1.444: 3 Chirality restraints: 2744 Sorted by residual: chirality pdb=" CB THR I 872 " pdb=" CA THR I 872 " pdb=" OG1 THR I 872 " pdb=" CG2 THR I 872 " both_signs ideal model delta sigma weight residual False 2.55 1.11 1.44 2.00e-01 2.50e+01 5.21e+01 chirality pdb=" CB THR C 872 " pdb=" CA THR C 872 " pdb=" OG1 THR C 872 " pdb=" CG2 THR C 872 " both_signs ideal model delta sigma weight residual False 2.55 1.14 1.41 2.00e-01 2.50e+01 5.00e+01 chirality pdb=" CB THR D 872 " pdb=" CA THR D 872 " pdb=" OG1 THR D 872 " pdb=" CG2 THR D 872 " both_signs ideal model delta sigma weight residual False 2.55 1.20 1.36 2.00e-01 2.50e+01 4.60e+01 ... (remaining 2741 not shown) Planarity restraints: 5058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 222 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO C 223 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 223 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 223 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 935 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO C 936 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 936 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 936 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 769 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO D 770 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 770 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 770 " 0.021 5.00e-02 4.00e+02 ... (remaining 5055 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.08: 517 2.08 - 2.71: 55979 2.71 - 3.34: 101329 3.34 - 3.97: 123672 3.97 - 4.60: 196133 Nonbonded interactions: 477630 Sorted by model distance: nonbonded pdb=" O CYS D 773 " pdb=" H LYS D 778 " model vdw 1.455 2.450 nonbonded pdb=" O CYS I 773 " pdb=" H LYS I 778 " model vdw 1.502 2.450 nonbonded pdb=" O CYS C 773 " pdb=" H LYS C 778 " model vdw 1.529 2.450 nonbonded pdb=" H LEU C 921 " pdb=" HA LEU C 921 " model vdw 1.578 1.816 nonbonded pdb="HE21 GLN D 932 " pdb=" OD1 ASN D 933 " model vdw 1.580 2.450 ... (remaining 477625 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 'E' } ncs_group { reference = (chain 'C' and (resid 157 through 954 or resid 1001 through 1002)) selection = chain 'D' selection = (chain 'I' and (resid 157 through 954 or resid 1001 through 1002)) } 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.620 Extract box with map and model: 1.260 Check model and map are aligned: 0.240 Set scattering table: 0.330 Process input model: 67.400 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.120 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 : 0.007 0.203 18068 Z= 0.325 Angle : 0.727 37.254 24619 Z= 0.335 Chirality : 0.069 1.444 2744 Planarity : 0.004 0.052 3051 Dihedral : 13.570 129.721 6858 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.68 % Favored : 95.14 % Rotamer: Outliers : 0.59 % Allowed : 4.99 % Favored : 94.42 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.55 % 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: 1.19 (0.19), residues: 2139 helix: 2.10 (0.17), residues: 1069 sheet: 1.65 (0.46), residues: 140 loop : -0.97 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 904 HIS 0.003 0.001 HIS D 434 PHE 0.008 0.001 PHE C 317 TYR 0.010 0.001 TYR I 756 ARG 0.003 0.000 ARG D 167 Details of bonding type rmsd link_BETA1-4 : bond 0.00793 ( 12) link_BETA1-4 : angle 1.98658 ( 36) hydrogen bonds : bond 0.22583 ( 901) hydrogen bonds : angle 7.21404 ( 2685) covalent geometry : bond 0.00651 (18056) covalent geometry : angle 0.72373 (24583) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 569 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 558 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 460 ASP cc_start: 0.7704 (m-30) cc_final: 0.7389 (m-30) REVERT: D 725 ILE cc_start: 0.7690 (mm) cc_final: 0.7478 (mm) REVERT: D 830 SER cc_start: 0.8944 (p) cc_final: 0.8672 (t) REVERT: I 281 ASP cc_start: 0.7560 (t0) cc_final: 0.7185 (t0) REVERT: I 625 ILE cc_start: 0.8834 (mt) cc_final: 0.8534 (mt) REVERT: I 819 ARG cc_start: 0.8344 (tpp-160) cc_final: 0.7966 (tpp80) REVERT: I 917 VAL cc_start: 0.8062 (t) cc_final: 0.7738 (t) REVERT: C 188 PHE cc_start: 0.8094 (m-80) cc_final: 0.7852 (m-10) REVERT: C 614 PHE cc_start: 0.8233 (m-80) cc_final: 0.8010 (m-10) outliers start: 11 outliers final: 3 residues processed: 565 average time/residue: 0.7644 time to fit residues: 626.4739 Evaluate side-chains 365 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 362 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain I residue 953 VAL Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 885 ASN C 714 GLN C 885 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.182297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.133087 restraints weight = 64393.901| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.98 r_work: 0.3471 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18068 Z= 0.170 Angle : 0.689 11.497 24619 Z= 0.358 Chirality : 0.070 1.446 2744 Planarity : 0.006 0.050 3051 Dihedral : 10.555 116.572 2812 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.19 % Favored : 94.62 % Rotamer: Outliers : 1.88 % Allowed : 12.94 % Favored : 85.19 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2139 helix: 1.52 (0.16), residues: 1116 sheet: 1.40 (0.44), residues: 139 loop : -1.02 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 954 HIS 0.010 0.001 HIS D 434 PHE 0.030 0.002 PHE I 913 TYR 0.016 0.001 TYR I 756 ARG 0.007 0.001 ARG C 537 Details of bonding type rmsd link_BETA1-4 : bond 0.00300 ( 12) link_BETA1-4 : angle 2.10828 ( 36) hydrogen bonds : bond 0.05723 ( 901) hydrogen bonds : angle 5.42140 ( 2685) covalent geometry : bond 0.00375 (18056) covalent geometry : angle 0.68504 (24583) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 410 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 375 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 186 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7979 (mm) REVERT: D 281 ASP cc_start: 0.8041 (t0) cc_final: 0.7823 (t0) REVERT: D 523 ILE cc_start: 0.9006 (mp) cc_final: 0.8769 (mp) REVERT: D 748 LEU cc_start: 0.8826 (tp) cc_final: 0.8602 (mp) REVERT: D 823 PHE cc_start: 0.8121 (t80) cc_final: 0.7579 (t80) REVERT: D 882 LEU cc_start: 0.8085 (tp) cc_final: 0.7875 (tp) REVERT: I 240 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8501 (ttt90) REVERT: I 281 ASP cc_start: 0.8116 (t0) cc_final: 0.7903 (t0) REVERT: I 460 ASP cc_start: 0.8040 (m-30) cc_final: 0.7833 (m-30) REVERT: I 685 CYS cc_start: 0.8828 (t) cc_final: 0.8550 (m) REVERT: I 879 THR cc_start: 0.8590 (m) cc_final: 0.8380 (p) REVERT: C 323 ILE cc_start: 0.8492 (pt) cc_final: 0.7635 (mt) outliers start: 35 outliers final: 20 residues processed: 396 average time/residue: 0.8220 time to fit residues: 496.9896 Evaluate side-chains 355 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 333 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 240 ARG Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 424 SER Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 775 LEU Chi-restraints excluded: chain I residue 784 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 830 SER Chi-restraints excluded: chain I residue 912 PHE Chi-restraints excluded: chain I residue 921 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 146 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 820 ASN ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.178273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128530 restraints weight = 64638.481| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.95 r_work: 0.3425 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 18068 Z= 0.167 Angle : 0.627 11.394 24619 Z= 0.324 Chirality : 0.069 1.439 2744 Planarity : 0.005 0.051 3051 Dihedral : 9.700 116.658 2809 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.96 % Favored : 94.86 % Rotamer: Outliers : 1.77 % Allowed : 14.76 % Favored : 83.47 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2139 helix: 1.57 (0.16), residues: 1123 sheet: 1.22 (0.45), residues: 130 loop : -1.10 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 954 HIS 0.007 0.001 HIS D 920 PHE 0.018 0.001 PHE I 187 TYR 0.013 0.001 TYR C 756 ARG 0.006 0.000 ARG D 394 Details of bonding type rmsd link_BETA1-4 : bond 0.00373 ( 12) link_BETA1-4 : angle 2.06078 ( 36) hydrogen bonds : bond 0.05474 ( 901) hydrogen bonds : angle 5.00961 ( 2685) covalent geometry : bond 0.00379 (18056) covalent geometry : angle 0.62268 (24583) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 378 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 345 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 186 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7925 (mm) REVERT: D 281 ASP cc_start: 0.8033 (t0) cc_final: 0.7808 (t0) REVERT: D 523 ILE cc_start: 0.9006 (mp) cc_final: 0.8798 (mp) REVERT: D 748 LEU cc_start: 0.8813 (tp) cc_final: 0.8604 (mp) REVERT: I 165 ILE cc_start: 0.7407 (mm) cc_final: 0.6996 (mm) REVERT: I 281 ASP cc_start: 0.8181 (t0) cc_final: 0.7968 (t0) REVERT: I 460 ASP cc_start: 0.8091 (m-30) cc_final: 0.7882 (m-30) REVERT: I 626 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8427 (tm-30) REVERT: I 685 CYS cc_start: 0.8831 (t) cc_final: 0.8617 (m) REVERT: I 819 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8138 (tpp80) REVERT: I 879 THR cc_start: 0.8588 (m) cc_final: 0.8384 (p) REVERT: C 188 PHE cc_start: 0.8086 (m-80) cc_final: 0.7833 (m-10) REVERT: C 323 ILE cc_start: 0.8578 (pt) cc_final: 0.7708 (mt) REVERT: C 431 TYR cc_start: 0.6588 (m-80) cc_final: 0.6317 (m-80) REVERT: C 614 PHE cc_start: 0.8409 (m-80) cc_final: 0.8122 (m-10) outliers start: 33 outliers final: 26 residues processed: 365 average time/residue: 0.7423 time to fit residues: 410.4767 Evaluate side-chains 353 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 326 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 830 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 424 SER Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 510 ILE Chi-restraints excluded: chain I residue 784 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 912 PHE Chi-restraints excluded: chain I residue 921 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 73 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 17 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 82 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 820 ASN ** 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 = 0.4133 r_free = 0.4133 target = 0.178315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.128681 restraints weight = 64489.807| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.96 r_work: 0.3426 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18068 Z= 0.130 Angle : 0.617 11.422 24619 Z= 0.313 Chirality : 0.069 1.441 2744 Planarity : 0.005 0.052 3051 Dihedral : 8.923 111.209 2809 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.14 % Favored : 94.67 % Rotamer: Outliers : 1.88 % Allowed : 15.14 % Favored : 82.98 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2139 helix: 1.62 (0.16), residues: 1135 sheet: 1.07 (0.44), residues: 130 loop : -1.04 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 954 HIS 0.006 0.001 HIS D 434 PHE 0.016 0.001 PHE I 913 TYR 0.018 0.001 TYR I 489 ARG 0.007 0.000 ARG D 394 Details of bonding type rmsd link_BETA1-4 : bond 0.00461 ( 12) link_BETA1-4 : angle 2.25805 ( 36) hydrogen bonds : bond 0.04676 ( 901) hydrogen bonds : angle 4.72131 ( 2685) covalent geometry : bond 0.00287 (18056) covalent geometry : angle 0.61132 (24583) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 378 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 343 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 186 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7946 (mm) REVERT: D 191 ARG cc_start: 0.8200 (mmm-85) cc_final: 0.7808 (mmm-85) REVERT: D 234 ILE cc_start: 0.8955 (mp) cc_final: 0.8736 (pt) REVERT: D 281 ASP cc_start: 0.7970 (t0) cc_final: 0.7763 (t0) REVERT: D 486 ASP cc_start: 0.7758 (m-30) cc_final: 0.7546 (p0) REVERT: D 523 ILE cc_start: 0.8964 (mp) cc_final: 0.8738 (mp) REVERT: D 823 PHE cc_start: 0.8284 (t80) cc_final: 0.7904 (t80) REVERT: D 882 LEU cc_start: 0.8082 (tp) cc_final: 0.7862 (tp) REVERT: I 165 ILE cc_start: 0.7386 (mm) cc_final: 0.6972 (mm) REVERT: I 281 ASP cc_start: 0.8138 (t0) cc_final: 0.7936 (t0) REVERT: I 460 ASP cc_start: 0.8089 (m-30) cc_final: 0.7885 (m-30) REVERT: I 685 CYS cc_start: 0.8797 (t) cc_final: 0.8593 (m) REVERT: I 819 ARG cc_start: 0.8562 (tpp-160) cc_final: 0.8100 (tpp80) REVERT: I 823 PHE cc_start: 0.8293 (t80) cc_final: 0.7960 (t80) REVERT: C 191 ARG cc_start: 0.8600 (ttm-80) cc_final: 0.7987 (tpt90) REVERT: C 323 ILE cc_start: 0.8560 (pt) cc_final: 0.7720 (mt) REVERT: C 834 PHE cc_start: 0.8054 (m-80) cc_final: 0.7628 (m-10) outliers start: 35 outliers final: 24 residues processed: 365 average time/residue: 0.8450 time to fit residues: 473.4306 Evaluate side-chains 347 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 322 time to evaluate : 6.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 424 SER Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 459 LEU Chi-restraints excluded: chain I residue 784 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 912 PHE Chi-restraints excluded: chain I residue 921 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 66 optimal weight: 20.0000 chunk 161 optimal weight: 0.0270 chunk 152 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 201 optimal weight: 0.9980 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 524 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 = 0.4098 r_free = 0.4098 target = 0.174964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127826 restraints weight = 64760.240| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.04 r_work: 0.3375 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18068 Z= 0.177 Angle : 0.621 11.420 24619 Z= 0.319 Chirality : 0.069 1.446 2744 Planarity : 0.005 0.066 3051 Dihedral : 8.189 111.905 2809 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.42 % Favored : 94.39 % Rotamer: Outliers : 2.25 % Allowed : 14.55 % Favored : 83.20 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2139 helix: 1.56 (0.16), residues: 1143 sheet: 0.59 (0.45), residues: 132 loop : -1.09 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 954 HIS 0.007 0.001 HIS D 434 PHE 0.014 0.001 PHE D 726 TYR 0.014 0.001 TYR C 756 ARG 0.007 0.000 ARG D 394 Details of bonding type rmsd link_BETA1-4 : bond 0.00288 ( 12) link_BETA1-4 : angle 2.52505 ( 36) hydrogen bonds : bond 0.04571 ( 901) hydrogen bonds : angle 4.57720 ( 2685) covalent geometry : bond 0.00398 (18056) covalent geometry : angle 0.61400 (24583) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 330 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 191 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7870 (mmm-85) REVERT: D 234 ILE cc_start: 0.8957 (mp) cc_final: 0.8718 (pt) REVERT: D 486 ASP cc_start: 0.8097 (m-30) cc_final: 0.7797 (p0) REVERT: I 165 ILE cc_start: 0.7520 (mm) cc_final: 0.7104 (mm) REVERT: I 323 ILE cc_start: 0.8569 (pt) cc_final: 0.7677 (mt) REVERT: I 819 ARG cc_start: 0.8597 (tpp-160) cc_final: 0.8129 (tpp80) REVERT: I 837 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8383 (m-80) REVERT: C 188 PHE cc_start: 0.8057 (m-80) cc_final: 0.7802 (m-10) REVERT: C 191 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.7976 (tpt90) REVERT: C 323 ILE cc_start: 0.8675 (pt) cc_final: 0.7787 (mt) REVERT: C 431 TYR cc_start: 0.6975 (m-80) cc_final: 0.6656 (m-80) REVERT: C 614 PHE cc_start: 0.8377 (m-80) cc_final: 0.8142 (m-10) REVERT: C 834 PHE cc_start: 0.8277 (m-80) cc_final: 0.7832 (m-10) outliers start: 42 outliers final: 30 residues processed: 355 average time/residue: 0.7031 time to fit residues: 372.9399 Evaluate side-chains 345 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 314 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain I residue 222 PHE Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 341 ASP Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 424 SER Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 459 LEU Chi-restraints excluded: chain I residue 510 ILE Chi-restraints excluded: chain I residue 784 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 837 PHE Chi-restraints excluded: chain I residue 912 PHE Chi-restraints excluded: chain I residue 921 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 714 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 8 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.173510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122973 restraints weight = 64219.066| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.91 r_work: 0.3348 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18068 Z= 0.180 Angle : 0.620 11.412 24619 Z= 0.320 Chirality : 0.069 1.445 2744 Planarity : 0.005 0.074 3051 Dihedral : 7.982 112.311 2809 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.47 % Favored : 94.34 % Rotamer: Outliers : 2.31 % Allowed : 15.14 % Favored : 82.56 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2139 helix: 1.53 (0.15), residues: 1149 sheet: 0.45 (0.46), residues: 132 loop : -1.15 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 954 HIS 0.007 0.001 HIS D 434 PHE 0.031 0.001 PHE I 913 TYR 0.019 0.001 TYR I 173 ARG 0.011 0.000 ARG I 394 Details of bonding type rmsd link_BETA1-4 : bond 0.00187 ( 12) link_BETA1-4 : angle 2.01606 ( 36) hydrogen bonds : bond 0.04393 ( 901) hydrogen bonds : angle 4.49102 ( 2685) covalent geometry : bond 0.00412 (18056) covalent geometry : angle 0.61557 (24583) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 375 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 332 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 191 ARG cc_start: 0.8213 (mmm-85) cc_final: 0.7797 (mmm-85) REVERT: D 234 ILE cc_start: 0.8946 (mp) cc_final: 0.8714 (pt) REVERT: I 632 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7562 (p0) REVERT: I 819 ARG cc_start: 0.8578 (tpp-160) cc_final: 0.8135 (tpp80) REVERT: I 837 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: C 188 PHE cc_start: 0.8076 (m-80) cc_final: 0.7803 (m-10) REVERT: C 191 ARG cc_start: 0.8605 (ttm-80) cc_final: 0.7984 (tpt90) REVERT: C 306 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6979 (mm-30) REVERT: C 431 TYR cc_start: 0.7079 (m-80) cc_final: 0.6765 (m-80) REVERT: C 614 PHE cc_start: 0.8426 (m-80) cc_final: 0.8211 (m-10) outliers start: 43 outliers final: 30 residues processed: 357 average time/residue: 0.6885 time to fit residues: 368.7170 Evaluate side-chains 348 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 316 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain I residue 222 PHE Chi-restraints excluded: chain I residue 341 ASP Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 424 SER Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 510 ILE Chi-restraints excluded: chain I residue 632 ASN Chi-restraints excluded: chain I residue 784 LEU Chi-restraints excluded: chain I residue 806 GLU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 820 ASN Chi-restraints excluded: chain I residue 837 PHE Chi-restraints excluded: chain I residue 912 PHE Chi-restraints excluded: chain I residue 921 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 714 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 23 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 199 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 820 ASN ** 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 = 0.4075 r_free = 0.4075 target = 0.172751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.127863 restraints weight = 64202.654| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.23 r_work: 0.3318 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18068 Z= 0.167 Angle : 0.611 11.426 24619 Z= 0.315 Chirality : 0.069 1.445 2744 Planarity : 0.005 0.064 3051 Dihedral : 7.244 112.215 2809 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.70 % Favored : 94.11 % Rotamer: Outliers : 2.04 % Allowed : 15.57 % Favored : 82.39 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2139 helix: 1.55 (0.15), residues: 1154 sheet: 0.11 (0.45), residues: 142 loop : -1.15 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 954 HIS 0.007 0.001 HIS D 434 PHE 0.019 0.001 PHE I 913 TYR 0.026 0.001 TYR C 528 ARG 0.008 0.000 ARG C 243 Details of bonding type rmsd link_BETA1-4 : bond 0.00229 ( 12) link_BETA1-4 : angle 2.04818 ( 36) hydrogen bonds : bond 0.04298 ( 901) hydrogen bonds : angle 4.39930 ( 2685) covalent geometry : bond 0.00381 (18056) covalent geometry : angle 0.60610 (24583) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 332 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 323 ILE cc_start: 0.8473 (pt) cc_final: 0.7559 (mt) REVERT: I 819 ARG cc_start: 0.8552 (tpp-160) cc_final: 0.8107 (tpp80) REVERT: I 837 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: C 323 ILE cc_start: 0.8599 (pt) cc_final: 0.7776 (mt) REVERT: C 431 TYR cc_start: 0.7191 (m-80) cc_final: 0.6860 (m-80) outliers start: 38 outliers final: 31 residues processed: 355 average time/residue: 0.7257 time to fit residues: 390.4132 Evaluate side-chains 352 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 320 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 690 SER Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain I residue 222 PHE Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 341 ASP Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 424 SER Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 510 ILE Chi-restraints excluded: chain I residue 784 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 820 ASN Chi-restraints excluded: chain I residue 837 PHE Chi-restraints excluded: chain I residue 912 PHE Chi-restraints excluded: chain I residue 921 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 714 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 GLU Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 65 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 463 HIS ** C 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.169319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118083 restraints weight = 64289.690| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.87 r_work: 0.3286 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 18068 Z= 0.260 Angle : 0.650 11.412 24619 Z= 0.340 Chirality : 0.070 1.452 2744 Planarity : 0.005 0.084 3051 Dihedral : 7.391 112.024 2809 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.84 % Favored : 93.97 % Rotamer: Outliers : 1.88 % Allowed : 16.16 % Favored : 81.96 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2139 helix: 1.34 (0.15), residues: 1151 sheet: -0.29 (0.44), residues: 147 loop : -1.26 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 954 HIS 0.008 0.001 HIS D 434 PHE 0.044 0.001 PHE I 913 TYR 0.026 0.002 TYR I 489 ARG 0.014 0.001 ARG I 394 Details of bonding type rmsd link_BETA1-4 : bond 0.00278 ( 12) link_BETA1-4 : angle 1.92753 ( 36) hydrogen bonds : bond 0.04430 ( 901) hydrogen bonds : angle 4.49208 ( 2685) covalent geometry : bond 0.00598 (18056) covalent geometry : angle 0.64591 (24583) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 366 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 331 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 630 MET cc_start: 0.8630 (mmm) cc_final: 0.8358 (mmm) REVERT: I 770 PRO cc_start: 0.6982 (Cg_exo) cc_final: 0.6726 (Cg_endo) REVERT: I 819 ARG cc_start: 0.8637 (tpp-160) cc_final: 0.8174 (tpp80) REVERT: I 837 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8543 (m-80) REVERT: C 188 PHE cc_start: 0.8251 (m-80) cc_final: 0.7856 (m-10) REVERT: C 486 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7840 (p0) outliers start: 35 outliers final: 30 residues processed: 353 average time/residue: 0.6927 time to fit residues: 363.1039 Evaluate side-chains 356 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 324 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 690 SER Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain I residue 222 PHE Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 424 SER Chi-restraints excluded: chain I residue 510 ILE Chi-restraints excluded: chain I residue 784 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 820 ASN Chi-restraints excluded: chain I residue 837 PHE Chi-restraints excluded: chain I residue 912 PHE Chi-restraints excluded: chain I residue 921 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 714 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 921 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 49 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 0.0770 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 820 ASN ** 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 = 0.4067 r_free = 0.4067 target = 0.171988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.120973 restraints weight = 63764.631| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.91 r_work: 0.3316 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18068 Z= 0.128 Angle : 0.602 11.378 24619 Z= 0.310 Chirality : 0.069 1.430 2744 Planarity : 0.005 0.073 3051 Dihedral : 7.229 112.778 2805 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.38 % Favored : 94.44 % Rotamer: Outliers : 1.40 % Allowed : 16.96 % Favored : 81.64 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2139 helix: 1.57 (0.15), residues: 1158 sheet: -0.13 (0.45), residues: 141 loop : -1.20 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 954 HIS 0.005 0.001 HIS D 434 PHE 0.029 0.001 PHE I 913 TYR 0.015 0.001 TYR C 528 ARG 0.011 0.000 ARG C 394 Details of bonding type rmsd link_BETA1-4 : bond 0.00303 ( 12) link_BETA1-4 : angle 1.64996 ( 36) hydrogen bonds : bond 0.04162 ( 901) hydrogen bonds : angle 4.31748 ( 2685) covalent geometry : bond 0.00293 (18056) covalent geometry : angle 0.59944 (24583) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 353 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 327 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 523 ILE cc_start: 0.8912 (mp) cc_final: 0.8575 (mp) REVERT: D 824 TRP cc_start: 0.8070 (t60) cc_final: 0.7783 (t60) REVERT: I 630 MET cc_start: 0.8509 (mmm) cc_final: 0.8280 (mmm) REVERT: I 770 PRO cc_start: 0.6914 (Cg_exo) cc_final: 0.6688 (Cg_endo) REVERT: I 819 ARG cc_start: 0.8503 (tpp-160) cc_final: 0.8050 (tpp80) REVERT: I 837 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8410 (m-80) REVERT: C 188 PHE cc_start: 0.8232 (m-80) cc_final: 0.7851 (m-10) REVERT: C 394 ARG cc_start: 0.8687 (ttm110) cc_final: 0.8284 (mtm110) outliers start: 26 outliers final: 25 residues processed: 341 average time/residue: 0.6831 time to fit residues: 347.0732 Evaluate side-chains 343 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 317 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain I residue 222 PHE Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 424 SER Chi-restraints excluded: chain I residue 510 ILE Chi-restraints excluded: chain I residue 784 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 820 ASN Chi-restraints excluded: chain I residue 837 PHE Chi-restraints excluded: chain I residue 912 PHE Chi-restraints excluded: chain I residue 921 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 714 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 820 ASN ** 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 = 0.4059 r_free = 0.4059 target = 0.171240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120144 restraints weight = 63852.282| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.90 r_work: 0.3311 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18068 Z= 0.156 Angle : 0.612 11.376 24619 Z= 0.315 Chirality : 0.069 1.433 2744 Planarity : 0.005 0.076 3051 Dihedral : 7.178 110.872 2805 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.56 % Favored : 94.25 % Rotamer: Outliers : 1.50 % Allowed : 17.07 % Favored : 81.43 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2139 helix: 1.57 (0.15), residues: 1167 sheet: -0.17 (0.45), residues: 141 loop : -1.18 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 954 HIS 0.006 0.001 HIS D 434 PHE 0.030 0.001 PHE I 913 TYR 0.016 0.001 TYR D 505 ARG 0.011 0.001 ARG I 394 Details of bonding type rmsd link_BETA1-4 : bond 0.00237 ( 12) link_BETA1-4 : angle 1.66224 ( 36) hydrogen bonds : bond 0.04086 ( 901) hydrogen bonds : angle 4.29436 ( 2685) covalent geometry : bond 0.00361 (18056) covalent geometry : angle 0.60867 (24583) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 320 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 188 PHE cc_start: 0.8192 (m-10) cc_final: 0.7885 (m-80) REVERT: D 523 ILE cc_start: 0.8952 (mp) cc_final: 0.8615 (mp) REVERT: D 824 TRP cc_start: 0.8150 (t60) cc_final: 0.7878 (t60) REVERT: I 323 ILE cc_start: 0.8544 (pt) cc_final: 0.7634 (mt) REVERT: I 630 MET cc_start: 0.8567 (mmm) cc_final: 0.8315 (mmm) REVERT: I 770 PRO cc_start: 0.6921 (Cg_exo) cc_final: 0.6672 (Cg_endo) REVERT: I 819 ARG cc_start: 0.8566 (tpp-160) cc_final: 0.8105 (tpp80) REVERT: I 837 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: C 188 PHE cc_start: 0.8196 (m-80) cc_final: 0.7796 (m-10) REVERT: C 323 ILE cc_start: 0.8677 (pt) cc_final: 0.7914 (mt) REVERT: C 394 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8301 (mtm110) outliers start: 28 outliers final: 23 residues processed: 336 average time/residue: 0.6969 time to fit residues: 350.7266 Evaluate side-chains 340 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 316 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain I residue 222 PHE Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 424 SER Chi-restraints excluded: chain I residue 510 ILE Chi-restraints excluded: chain I residue 784 LEU Chi-restraints excluded: chain I residue 820 ASN Chi-restraints excluded: chain I residue 837 PHE Chi-restraints excluded: chain I residue 912 PHE Chi-restraints excluded: chain I residue 921 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 714 GLN Chi-restraints excluded: chain C residue 813 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 159 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 211 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 820 ASN ** 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 = 0.4046 r_free = 0.4046 target = 0.170145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123094 restraints weight = 64320.453| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.03 r_work: 0.3303 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18068 Z= 0.178 Angle : 0.617 11.416 24619 Z= 0.319 Chirality : 0.069 1.445 2744 Planarity : 0.005 0.091 3051 Dihedral : 7.212 110.141 2805 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.89 % Favored : 93.92 % Rotamer: Outliers : 1.40 % Allowed : 17.39 % Favored : 81.21 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2139 helix: 1.52 (0.15), residues: 1174 sheet: -0.25 (0.45), residues: 146 loop : -1.20 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 916 HIS 0.007 0.001 HIS D 434 PHE 0.028 0.001 PHE I 913 TYR 0.016 0.001 TYR C 528 ARG 0.010 0.001 ARG C 394 Details of bonding type rmsd link_BETA1-4 : bond 0.00229 ( 12) link_BETA1-4 : angle 1.68731 ( 36) hydrogen bonds : bond 0.04057 ( 901) hydrogen bonds : angle 4.29715 ( 2685) covalent geometry : bond 0.00411 (18056) covalent geometry : angle 0.61387 (24583) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19458.47 seconds wall clock time: 339 minutes 17.61 seconds (20357.61 seconds total)