Starting phenix.real_space_refine on Tue Aug 26 07:06:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g2j_29679/08_2025/8g2j_29679_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g2j_29679/08_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_29679/08_2025/8g2j_29679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g2j_29679/08_2025/8g2j_29679.map" model { file = "/net/cci-nas-00/data/ceres_data/8g2j_29679/08_2025/8g2j_29679_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g2j_29679/08_2025/8g2j_29679_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.12, per 1000 atoms: 0.15 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: 2.40 Conformation dependent library (CDL) restraints added in 945.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.03 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: 6.86 Time building geometry restraints manager: 3.30 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 27.220 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.580 ------------------------------------------------------------------------------- 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 : 8.68 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG D 167 TYR 0.010 0.001 TYR I 756 PHE 0.008 0.001 PHE C 317 TRP 0.007 0.001 TRP I 904 HIS 0.003 0.001 HIS D 434 Details of bonding type rmsd covalent geometry : bond 0.00651 (18056) covalent geometry : angle 0.72373 (24583) hydrogen bonds : bond 0.22583 ( 901) hydrogen bonds : angle 7.21404 ( 2685) link_BETA1-4 : bond 0.00793 ( 12) link_BETA1-4 : angle 1.98658 ( 36) *********************** 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 : 0.887 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: 0.7476 (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: 0.7830 (t) REVERT: C 188 PHE cc_start: 0.8094 (m-80) cc_final: 0.7853 (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: 0.3162 time to fit residues: 257.8254 Evaluate side-chains 364 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 361 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0020 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 overall best weight: 1.1192 ------------------------------------------------------------------------------- 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** D 885 ASN I 885 ASN C 714 GLN C 885 ASN C 920 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.182310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.132995 restraints weight = 64674.295| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.99 r_work: 0.3475 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18068 Z= 0.175 Angle : 0.679 11.477 24619 Z= 0.354 Chirality : 0.070 1.444 2744 Planarity : 0.005 0.050 3051 Dihedral : 10.754 118.407 2812 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.10 % Favored : 94.72 % Rotamer: Outliers : 1.88 % Allowed : 12.94 % Favored : 85.19 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.18), residues: 2139 helix: 1.54 (0.16), residues: 1116 sheet: 1.45 (0.44), residues: 139 loop : -1.02 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 537 TYR 0.015 0.001 TYR I 756 PHE 0.031 0.002 PHE I 913 TRP 0.014 0.001 TRP C 871 HIS 0.010 0.001 HIS D 434 Details of bonding type rmsd covalent geometry : bond 0.00379 (18056) covalent geometry : angle 0.67501 (24583) hydrogen bonds : bond 0.06198 ( 901) hydrogen bonds : angle 5.49303 ( 2685) link_BETA1-4 : bond 0.00398 ( 12) link_BETA1-4 : angle 2.09732 ( 36) *********************** 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 402 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 367 time to evaluate : 0.713 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: 0.8145 (OUTLIER) cc_final: 0.7924 (mm) REVERT: D 281 ASP cc_start: 0.8044 (t0) cc_final: 0.7821 (t0) REVERT: D 523 ILE cc_start: 0.9030 (mp) cc_final: 0.8795 (mp) REVERT: D 748 LEU cc_start: 0.8822 (tp) cc_final: 0.8615 (mp) REVERT: I 281 ASP cc_start: 0.8123 (t0) cc_final: 0.7899 (t0) REVERT: I 460 ASP cc_start: 0.8038 (m-30) cc_final: 0.7828 (m-30) REVERT: I 685 CYS cc_start: 0.8816 (t) cc_final: 0.8539 (m) REVERT: I 819 ARG cc_start: 0.8559 (tpp-160) cc_final: 0.8090 (tpp80) REVERT: I 879 THR cc_start: 0.8583 (m) cc_final: 0.8369 (p) REVERT: C 323 ILE cc_start: 0.8495 (pt) cc_final: 0.7643 (mt) REVERT: C 614 PHE cc_start: 0.8241 (m-80) cc_final: 0.7955 (m-10) outliers start: 35 outliers final: 22 residues processed: 389 average time/residue: 0.2923 time to fit residues: 169.6769 Evaluate side-chains 353 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 330 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 425 ARG 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 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 920 HIS 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 55 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 194 optimal weight: 0.3980 chunk 114 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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** ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 920 HIS ** 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 = 0.4085 r_free = 0.4085 target = 0.173415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125938 restraints weight = 64610.327| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.11 r_work: 0.3346 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 18068 Z= 0.271 Angle : 0.686 11.465 24619 Z= 0.360 Chirality : 0.071 1.462 2744 Planarity : 0.005 0.057 3051 Dihedral : 9.962 118.799 2809 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.70 % Favored : 94.11 % Rotamer: Outliers : 2.31 % Allowed : 14.39 % Favored : 83.31 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.18), residues: 2139 helix: 1.29 (0.15), residues: 1135 sheet: 0.80 (0.46), residues: 132 loop : -1.16 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 394 TYR 0.013 0.002 TYR D 338 PHE 0.017 0.002 PHE I 187 TRP 0.013 0.002 TRP I 388 HIS 0.030 0.002 HIS C 920 Details of bonding type rmsd covalent geometry : bond 0.00619 (18056) covalent geometry : angle 0.68106 (24583) hydrogen bonds : bond 0.05609 ( 901) hydrogen bonds : angle 5.08962 ( 2685) link_BETA1-4 : bond 0.00439 ( 12) link_BETA1-4 : angle 2.27673 ( 36) *********************** 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 396 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 353 time to evaluate : 0.721 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 281 ASP cc_start: 0.8225 (t0) cc_final: 0.7962 (t0) REVERT: D 486 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7792 (p0) REVERT: D 823 PHE cc_start: 0.8366 (t80) cc_final: 0.8002 (t80) REVERT: D 824 TRP cc_start: 0.7905 (t60) cc_final: 0.7669 (t60) REVERT: I 281 ASP cc_start: 0.8340 (t0) cc_final: 0.8109 (t0) REVERT: I 460 ASP cc_start: 0.8437 (m-30) cc_final: 0.8232 (m-30) REVERT: I 733 PHE cc_start: 0.8411 (m-80) cc_final: 0.8127 (m-80) REVERT: I 819 ARG cc_start: 0.8625 (tpp-160) cc_final: 0.8138 (tpp80) REVERT: I 823 PHE cc_start: 0.8247 (t80) cc_final: 0.7968 (t80) REVERT: I 879 THR cc_start: 0.8624 (m) cc_final: 0.8417 (p) REVERT: C 191 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.7939 (tpt90) REVERT: C 323 ILE cc_start: 0.8705 (pt) cc_final: 0.7807 (mt) REVERT: C 431 TYR cc_start: 0.6986 (m-80) cc_final: 0.6719 (m-80) REVERT: C 614 PHE cc_start: 0.8279 (m-80) cc_final: 0.8031 (m-10) REVERT: C 821 GLU cc_start: 0.9018 (tp30) cc_final: 0.8799 (tp30) REVERT: C 834 PHE cc_start: 0.8151 (m-80) cc_final: 0.7741 (m-10) REVERT: C 920 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.5892 (t-170) outliers start: 43 outliers final: 29 residues processed: 381 average time/residue: 0.2864 time to fit residues: 163.9077 Evaluate side-chains 354 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 323 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 830 SER Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 307 THR Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 424 SER 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 202 LEU 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 920 HIS 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 212 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 154 optimal weight: 0.6980 chunk 139 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.170955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123810 restraints weight = 64190.696| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.01 r_work: 0.3281 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18068 Z= 0.242 Angle : 0.668 11.468 24619 Z= 0.345 Chirality : 0.070 1.462 2744 Planarity : 0.005 0.063 3051 Dihedral : 9.345 115.725 2809 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.52 % Favored : 94.30 % Rotamer: Outliers : 2.47 % Allowed : 14.60 % Favored : 82.93 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.18), residues: 2139 helix: 1.18 (0.15), residues: 1139 sheet: 0.12 (0.46), residues: 132 loop : -1.33 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 191 TYR 0.013 0.002 TYR D 756 PHE 0.016 0.001 PHE I 913 TRP 0.014 0.001 TRP D 954 HIS 0.008 0.002 HIS D 434 Details of bonding type rmsd covalent geometry : bond 0.00547 (18056) covalent geometry : angle 0.66140 (24583) hydrogen bonds : bond 0.04944 ( 901) hydrogen bonds : angle 4.86771 ( 2685) link_BETA1-4 : bond 0.00323 ( 12) link_BETA1-4 : angle 2.46005 ( 36) *********************** 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 374 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 328 time to evaluate : 0.802 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: D 191 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.8035 (mmm-85) REVERT: D 486 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7548 (p0) REVERT: D 823 PHE cc_start: 0.8384 (t80) cc_final: 0.8021 (t80) REVERT: I 460 ASP cc_start: 0.8214 (m-30) cc_final: 0.8000 (m-30) REVERT: I 819 ARG cc_start: 0.8566 (tpp-160) cc_final: 0.8102 (tpp80) REVERT: I 823 PHE cc_start: 0.8338 (t80) cc_final: 0.8113 (t80) REVERT: I 837 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8389 (m-80) REVERT: C 188 PHE cc_start: 0.8290 (m-80) cc_final: 0.7950 (m-10) REVERT: C 431 TYR cc_start: 0.7252 (m-80) cc_final: 0.6952 (m-80) outliers start: 46 outliers final: 32 residues processed: 356 average time/residue: 0.2928 time to fit residues: 155.2272 Evaluate side-chains 348 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 314 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 307 THR Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 486 ASP 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 769 ILE Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain I residue 341 ASP Chi-restraints excluded: chain I residue 424 SER 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 820 ASN Chi-restraints excluded: chain I residue 830 SER 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 813 SER Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 920 HIS 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 92 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 98 optimal weight: 0.0870 chunk 212 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.172420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121040 restraints weight = 63868.033| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.96 r_work: 0.3321 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4562 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= 0.147 Angle : 0.621 11.397 24619 Z= 0.318 Chirality : 0.069 1.439 2744 Planarity : 0.005 0.058 3051 Dihedral : 8.832 117.085 2809 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.10 % Favored : 94.72 % Rotamer: Outliers : 2.09 % Allowed : 15.24 % Favored : 82.66 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.18), residues: 2139 helix: 1.38 (0.15), residues: 1143 sheet: -0.08 (0.44), residues: 142 loop : -1.27 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 394 TYR 0.019 0.001 TYR I 489 PHE 0.013 0.001 PHE I 187 TRP 0.013 0.001 TRP D 954 HIS 0.006 0.001 HIS D 434 Details of bonding type rmsd covalent geometry : bond 0.00332 (18056) covalent geometry : angle 0.61565 (24583) hydrogen bonds : bond 0.04658 ( 901) hydrogen bonds : angle 4.63386 ( 2685) link_BETA1-4 : bond 0.00386 ( 12) link_BETA1-4 : angle 2.20938 ( 36) *********************** 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 365 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 326 time to evaluate : 0.686 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: 0.8191 (mmm-85) cc_final: 0.7915 (mmm-85) REVERT: D 486 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7541 (p0) REVERT: D 823 PHE cc_start: 0.8354 (t80) cc_final: 0.8000 (t80) REVERT: I 399 MET cc_start: 0.8432 (ptm) cc_final: 0.8185 (ptp) REVERT: I 460 ASP cc_start: 0.8168 (m-30) cc_final: 0.7955 (m-30) REVERT: I 819 ARG cc_start: 0.8566 (tpp-160) cc_final: 0.8109 (tpp80) REVERT: I 837 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: C 188 PHE cc_start: 0.8273 (m-80) cc_final: 0.7939 (m-10) REVERT: C 431 TYR cc_start: 0.7202 (m-80) cc_final: 0.6901 (m-80) REVERT: C 486 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7372 (p0) outliers start: 39 outliers final: 29 residues processed: 346 average time/residue: 0.2884 time to fit residues: 149.4176 Evaluate side-chains 346 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 314 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 404 LEU Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 486 ASP 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 769 ILE Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain I residue 222 PHE Chi-restraints excluded: chain I residue 424 SER 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 261 ASP 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 920 HIS 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 11 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.170685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125179 restraints weight = 63941.656| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.37 r_work: 0.3279 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18068 Z= 0.187 Angle : 0.632 11.421 24619 Z= 0.324 Chirality : 0.069 1.449 2744 Planarity : 0.005 0.060 3051 Dihedral : 8.277 115.029 2809 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.70 % Favored : 94.11 % Rotamer: Outliers : 1.88 % Allowed : 15.94 % Favored : 82.18 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.18), residues: 2139 helix: 1.38 (0.15), residues: 1145 sheet: -0.27 (0.44), residues: 142 loop : -1.30 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 243 TYR 0.013 0.001 TYR I 489 PHE 0.038 0.001 PHE I 913 TRP 0.013 0.001 TRP D 954 HIS 0.007 0.001 HIS D 434 Details of bonding type rmsd covalent geometry : bond 0.00425 (18056) covalent geometry : angle 0.62571 (24583) hydrogen bonds : bond 0.04515 ( 901) hydrogen bonds : angle 4.55622 ( 2685) link_BETA1-4 : bond 0.00210 ( 12) link_BETA1-4 : angle 2.34889 ( 36) *********************** 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 367 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 332 time to evaluate : 0.693 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: D 486 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7659 (p0) REVERT: I 399 MET cc_start: 0.8466 (ptm) cc_final: 0.8236 (ptp) REVERT: I 460 ASP cc_start: 0.8211 (m-30) cc_final: 0.8010 (m-30) REVERT: I 819 ARG cc_start: 0.8569 (tpp-160) cc_final: 0.8112 (tpp80) REVERT: I 837 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: I 929 MET cc_start: 0.7610 (ptm) cc_final: 0.7364 (ptm) REVERT: C 188 PHE cc_start: 0.8252 (m-80) cc_final: 0.7945 (m-10) REVERT: C 323 ILE cc_start: 0.8616 (pt) cc_final: 0.7783 (mt) REVERT: C 431 TYR cc_start: 0.7384 (m-80) cc_final: 0.7076 (m-80) REVERT: C 486 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7531 (p0) REVERT: C 921 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8239 (tt) outliers start: 35 outliers final: 27 residues processed: 353 average time/residue: 0.2797 time to fit residues: 148.2600 Evaluate side-chains 351 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 320 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 425 ARG Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 767 CYS Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain I residue 222 PHE 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 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 912 PHE 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 41 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.171081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119517 restraints weight = 64048.278| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.92 r_work: 0.3301 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18068 Z= 0.164 Angle : 0.614 11.437 24619 Z= 0.316 Chirality : 0.069 1.444 2744 Planarity : 0.005 0.076 3051 Dihedral : 7.253 114.932 2809 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.42 % Favored : 94.39 % Rotamer: Outliers : 1.77 % Allowed : 16.05 % Favored : 82.18 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.18), residues: 2139 helix: 1.47 (0.15), residues: 1145 sheet: -0.28 (0.44), residues: 142 loop : -1.28 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 394 TYR 0.019 0.001 TYR I 489 PHE 0.021 0.001 PHE I 913 TRP 0.012 0.001 TRP D 954 HIS 0.006 0.001 HIS D 434 Details of bonding type rmsd covalent geometry : bond 0.00375 (18056) covalent geometry : angle 0.60889 (24583) hydrogen bonds : bond 0.04368 ( 901) hydrogen bonds : angle 4.44391 ( 2685) link_BETA1-4 : bond 0.00318 ( 12) link_BETA1-4 : angle 2.12720 ( 36) *********************** 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 369 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 336 time to evaluate : 0.923 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: D 486 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7638 (p0) REVERT: I 399 MET cc_start: 0.8476 (ptm) cc_final: 0.8234 (ptp) REVERT: I 819 ARG cc_start: 0.8566 (tpp-160) cc_final: 0.8110 (tpp80) REVERT: I 837 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8440 (m-80) REVERT: I 929 MET cc_start: 0.7419 (ptm) cc_final: 0.7118 (ptm) REVERT: C 188 PHE cc_start: 0.8224 (m-80) cc_final: 0.7918 (m-10) REVERT: C 431 TYR cc_start: 0.7366 (m-80) cc_final: 0.7052 (m-80) REVERT: C 486 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7530 (p0) outliers start: 33 outliers final: 26 residues processed: 357 average time/residue: 0.2821 time to fit residues: 150.1541 Evaluate side-chains 347 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 318 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 425 ARG Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain I residue 222 PHE 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 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 926 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 132 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.171839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120666 restraints weight = 63625.738| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.90 r_work: 0.3312 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18068 Z= 0.128 Angle : 0.594 11.350 24619 Z= 0.306 Chirality : 0.068 1.429 2744 Planarity : 0.005 0.068 3051 Dihedral : 7.034 114.040 2809 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.96 % Favored : 94.86 % Rotamer: Outliers : 1.66 % Allowed : 16.53 % Favored : 81.80 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.18), residues: 2139 helix: 1.63 (0.16), residues: 1145 sheet: -0.15 (0.45), residues: 141 loop : -1.23 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 394 TYR 0.014 0.001 TYR I 489 PHE 0.034 0.001 PHE I 913 TRP 0.012 0.001 TRP D 954 HIS 0.005 0.001 HIS D 434 Details of bonding type rmsd covalent geometry : bond 0.00293 (18056) covalent geometry : angle 0.59161 (24583) hydrogen bonds : bond 0.04193 ( 901) hydrogen bonds : angle 4.33977 ( 2685) link_BETA1-4 : bond 0.00367 ( 12) link_BETA1-4 : angle 1.63975 ( 36) *********************** 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 362 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 331 time to evaluate : 0.673 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: symmetry clash revert: symmetry clash REVERT: I 323 ILE cc_start: 0.8575 (pt) cc_final: 0.7677 (mt) REVERT: I 399 MET cc_start: 0.8655 (ptm) cc_final: 0.8374 (ptp) REVERT: I 770 PRO cc_start: 0.6944 (Cg_exo) cc_final: 0.6721 (Cg_endo) REVERT: I 819 ARG cc_start: 0.8575 (tpp-160) cc_final: 0.8110 (tpp80) REVERT: I 837 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8531 (m-80) REVERT: I 929 MET cc_start: 0.7408 (ptm) cc_final: 0.7122 (ptm) REVERT: C 188 PHE cc_start: 0.8167 (m-80) cc_final: 0.7877 (m-10) REVERT: C 323 ILE cc_start: 0.8674 (pt) cc_final: 0.7864 (mt) outliers start: 31 outliers final: 25 residues processed: 350 average time/residue: 0.2794 time to fit residues: 145.8768 Evaluate side-chains 346 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 320 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 468 SER Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain I residue 222 PHE 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 161 ILE Chi-restraints excluded: chain C residue 202 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 921 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 43 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.171378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124560 restraints weight = 63672.514| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.99 r_work: 0.3309 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.003 0.049 18068 Z= 0.147 Angle : 0.603 11.359 24619 Z= 0.311 Chirality : 0.069 1.431 2744 Planarity : 0.005 0.071 3051 Dihedral : 6.752 111.380 2805 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.66 % Favored : 94.16 % Rotamer: Outliers : 1.56 % Allowed : 16.80 % Favored : 81.64 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.18), residues: 2139 helix: 1.64 (0.16), residues: 1152 sheet: -0.26 (0.45), residues: 142 loop : -1.24 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 243 TYR 0.014 0.001 TYR I 489 PHE 0.034 0.001 PHE I 913 TRP 0.012 0.001 TRP D 954 HIS 0.006 0.001 HIS D 434 Details of bonding type rmsd covalent geometry : bond 0.00336 (18056) covalent geometry : angle 0.59986 (24583) hydrogen bonds : bond 0.04131 ( 901) hydrogen bonds : angle 4.28032 ( 2685) link_BETA1-4 : bond 0.00262 ( 12) link_BETA1-4 : angle 1.73876 ( 36) *********************** 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 355 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 326 time to evaluate : 0.692 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: I 323 ILE cc_start: 0.8550 (pt) cc_final: 0.7606 (mt) REVERT: I 399 MET cc_start: 0.8654 (ptm) cc_final: 0.8395 (ptp) REVERT: I 630 MET cc_start: 0.8579 (mmm) cc_final: 0.8336 (mmm) REVERT: I 770 PRO cc_start: 0.6887 (Cg_exo) cc_final: 0.6646 (Cg_endo) REVERT: I 819 ARG cc_start: 0.8566 (tpp-160) cc_final: 0.8119 (tpp80) REVERT: I 837 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8566 (m-80) REVERT: C 188 PHE cc_start: 0.8152 (m-80) cc_final: 0.7863 (m-10) REVERT: C 323 ILE cc_start: 0.8667 (pt) cc_final: 0.7844 (mt) REVERT: C 486 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7742 (p0) REVERT: C 664 LYS cc_start: 0.8614 (mmtm) cc_final: 0.8298 (mtpt) outliers start: 29 outliers final: 26 residues processed: 343 average time/residue: 0.3019 time to fit residues: 153.7754 Evaluate side-chains 341 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 313 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 468 SER Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain I residue 222 PHE 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 161 ILE 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 714 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 GLU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 912 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 101 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 39 optimal weight: 0.0170 chunk 51 optimal weight: 3.9990 chunk 209 optimal weight: 0.2980 chunk 127 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 820 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.172772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126041 restraints weight = 63800.739| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.19 r_work: 0.3320 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5205 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= 0.116 Angle : 0.589 11.334 24619 Z= 0.303 Chirality : 0.068 1.422 2744 Planarity : 0.005 0.078 3051 Dihedral : 6.635 110.466 2805 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 1.40 % Allowed : 17.12 % Favored : 81.48 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.19), residues: 2139 helix: 1.74 (0.16), residues: 1164 sheet: -0.15 (0.45), residues: 142 loop : -1.19 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 394 TYR 0.018 0.001 TYR D 505 PHE 0.031 0.001 PHE I 913 TRP 0.015 0.001 TRP D 824 HIS 0.005 0.001 HIS D 434 Details of bonding type rmsd covalent geometry : bond 0.00264 (18056) covalent geometry : angle 0.58625 (24583) hydrogen bonds : bond 0.03970 ( 901) hydrogen bonds : angle 4.20115 ( 2685) link_BETA1-4 : bond 0.00337 ( 12) link_BETA1-4 : angle 1.53648 ( 36) ********************** 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 341 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 315 time to evaluate : 0.594 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: D 188 PHE cc_start: 0.8210 (m-10) cc_final: 0.7924 (m-80) REVERT: I 323 ILE cc_start: 0.8470 (pt) cc_final: 0.7503 (mt) REVERT: I 399 MET cc_start: 0.8508 (ptm) cc_final: 0.8239 (ptp) REVERT: I 630 MET cc_start: 0.8527 (mmm) cc_final: 0.8312 (mmm) REVERT: I 770 PRO cc_start: 0.6702 (Cg_exo) cc_final: 0.6454 (Cg_endo) REVERT: I 819 ARG cc_start: 0.8471 (tpp-160) cc_final: 0.8029 (tpp80) REVERT: I 837 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8443 (m-80) REVERT: C 188 PHE cc_start: 0.8160 (m-80) cc_final: 0.7884 (m-10) REVERT: C 323 ILE cc_start: 0.8584 (pt) cc_final: 0.7786 (mt) REVERT: C 523 ILE cc_start: 0.8890 (mp) cc_final: 0.8543 (mp) REVERT: C 664 LYS cc_start: 0.8522 (mmtm) cc_final: 0.8241 (mtpt) outliers start: 26 outliers final: 22 residues processed: 331 average time/residue: 0.2888 time to fit residues: 142.2709 Evaluate side-chains 329 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 306 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 468 SER Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain I residue 222 PHE Chi-restraints excluded: chain I residue 424 SER 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 161 ILE Chi-restraints excluded: chain C residue 202 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 26 optimal weight: 0.1980 chunk 57 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 123 optimal weight: 0.0570 chunk 51 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.173252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122439 restraints weight = 63455.138| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.87 r_work: 0.3342 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5296 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= 0.115 Angle : 0.584 11.342 24619 Z= 0.301 Chirality : 0.068 1.424 2744 Planarity : 0.005 0.085 3051 Dihedral : 6.516 108.278 2805 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.19 % Favored : 94.62 % Rotamer: Outliers : 1.29 % Allowed : 17.34 % Favored : 81.37 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.19), residues: 2139 helix: 1.85 (0.16), residues: 1158 sheet: -0.06 (0.45), residues: 141 loop : -1.20 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 394 TYR 0.015 0.001 TYR D 505 PHE 0.029 0.001 PHE I 913 TRP 0.017 0.001 TRP D 824 HIS 0.005 0.001 HIS D 434 Details of bonding type rmsd covalent geometry : bond 0.00262 (18056) covalent geometry : angle 0.58134 (24583) hydrogen bonds : bond 0.03893 ( 901) hydrogen bonds : angle 4.15483 ( 2685) link_BETA1-4 : bond 0.00335 ( 12) link_BETA1-4 : angle 1.50659 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7881.84 seconds wall clock time: 134 minutes 19.04 seconds (8059.04 seconds total)