Starting phenix.real_space_refine on Thu Feb 22 13:46:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2j_29679/02_2024/8g2j_29679_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2j_29679/02_2024/8g2j_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2j_29679/02_2024/8g2j_29679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2j_29679/02_2024/8g2j_29679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2j_29679/02_2024/8g2j_29679_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2j_29679/02_2024/8g2j_29679_trim.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 87 5.16 5 C 11437 2.51 5 N 2884 2.21 5 O 3132 1.98 5 H 16852 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 913": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 912": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34401 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 11356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 11356 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 673} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 11394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11394 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 675} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 11372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 11372 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 674} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' MG': 1, 'UPG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' MG': 1, 'UPG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' MG': 1, 'UPG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.92, per 1000 atoms: 0.46 Number of scatterers: 34401 At special positions: 0 Unit cell: (133.65, 130.35, 102.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 87 16.00 P 6 15.00 Mg 3 11.99 O 3132 8.00 N 2884 7.00 C 11437 6.00 H 16852 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 29.76 Conformation dependent library (CDL) restraints added in 3.7 seconds 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 11 sheets defined 57.9% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 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: 13.22 Time building geometry restraints manager: 30.68 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: 72.99 - 85.19: 82 85.19 - 97.40: 1 97.40 - 109.60: 23292 109.60 - 121.81: 33335 121.81 - 134.01: 6143 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 1.850 nonbonded pdb=" O CYS I 773 " pdb=" H LYS I 778 " model vdw 1.502 1.850 nonbonded pdb=" O CYS C 773 " pdb=" H LYS C 778 " model vdw 1.529 1.850 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 1.850 ... (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 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.570 Extract box with map and model: 8.950 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 112.050 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.090 ------------------------------------------------------------------------------- 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 18056 Z= 0.430 Angle : 0.724 37.254 24583 Z= 0.334 Chirality : 0.069 1.444 2744 Planarity : 0.004 0.052 3051 Dihedral : 13.570 129.721 6858 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.68 % Favored : 95.14 % Rotamer: Outliers : 0.59 % Allowed : 4.99 % Favored : 94.42 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.19), residues: 2139 helix: 2.10 (0.17), residues: 1069 sheet: 1.65 (0.46), residues: 140 loop : -0.97 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 904 HIS 0.003 0.001 HIS D 434 PHE 0.008 0.001 PHE C 317 TYR 0.010 0.001 TYR I 756 ARG 0.003 0.000 ARG D 167 *********************** 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 fitting. rotamer outliers: 11 poor density : 558 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 460 ASP cc_start: 0.7704 (m-30) cc_final: 0.7389 (m-30) REVERT: D 725 ILE cc_start: 0.7690 (mm) cc_final: 0.7478 (mm) REVERT: D 830 SER cc_start: 0.8944 (p) cc_final: 0.8672 (t) REVERT: I 281 ASP cc_start: 0.7560 (t0) cc_final: 0.7185 (t0) REVERT: I 625 ILE cc_start: 0.8834 (mt) cc_final: 0.8534 (mt) REVERT: I 819 ARG cc_start: 0.8344 (tpp-160) cc_final: 0.7966 (tpp80) REVERT: I 917 VAL cc_start: 0.8062 (t) cc_final: 0.7738 (t) REVERT: C 188 PHE cc_start: 0.8094 (m-80) cc_final: 0.7852 (m-10) REVERT: C 614 PHE cc_start: 0.8233 (m-80) cc_final: 0.8010 (m-10) outliers start: 11 outliers final: 3 residues processed: 565 average time/residue: 0.7485 time to fit residues: 606.1167 Evaluate side-chains 365 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 362 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain I residue 953 VAL Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 714 GLN I 885 ASN C 714 GLN C 885 ASN C 920 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18056 Z= 0.269 Angle : 0.672 11.484 24583 Z= 0.350 Chirality : 0.070 1.448 2744 Planarity : 0.005 0.049 3051 Dihedral : 10.747 118.154 2812 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.96 % Favored : 94.81 % Rotamer: Outliers : 2.15 % Allowed : 12.78 % Favored : 85.08 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2139 helix: 1.61 (0.16), residues: 1103 sheet: 1.51 (0.45), residues: 141 loop : -1.06 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 871 HIS 0.011 0.001 HIS D 434 PHE 0.030 0.002 PHE I 913 TYR 0.016 0.001 TYR I 756 ARG 0.008 0.001 ARG C 537 *********************** 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 fitting. rotamer outliers: 40 poor density : 362 time to evaluate : 2.915 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: D 186 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7975 (mm) REVERT: D 460 ASP cc_start: 0.7664 (m-30) cc_final: 0.7411 (m-30) REVERT: D 523 ILE cc_start: 0.9043 (mp) cc_final: 0.8808 (mp) REVERT: D 748 LEU cc_start: 0.8809 (tp) cc_final: 0.8600 (mp) REVERT: D 882 LEU cc_start: 0.8151 (tp) cc_final: 0.7939 (tp) REVERT: I 240 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8295 (ttt90) REVERT: C 191 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.7885 (tpt90) REVERT: C 323 ILE cc_start: 0.8354 (pt) cc_final: 0.7557 (mt) outliers start: 40 outliers final: 26 residues processed: 386 average time/residue: 0.6928 time to fit residues: 401.2522 Evaluate side-chains 349 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 321 time to evaluate : 2.772 ------------------------------------------------------------------------------- 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 514 ASP Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 632 ASN Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 240 ARG Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 424 SER Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 775 LEU Chi-restraints excluded: chain I residue 784 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 830 SER Chi-restraints excluded: chain I residue 912 PHE Chi-restraints excluded: chain I residue 921 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 953 VAL 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 108 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 820 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 18056 Z= 0.298 Angle : 0.634 11.450 24583 Z= 0.330 Chirality : 0.070 1.454 2744 Planarity : 0.005 0.053 3051 Dihedral : 9.886 118.171 2810 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.05 % Favored : 94.76 % Rotamer: Outliers : 2.36 % Allowed : 13.90 % Favored : 83.74 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.18), residues: 2139 helix: 1.49 (0.15), residues: 1135 sheet: 1.29 (0.45), residues: 130 loop : -1.12 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 954 HIS 0.023 0.002 HIS C 920 PHE 0.018 0.001 PHE D 187 TYR 0.011 0.001 TYR C 756 ARG 0.008 0.001 ARG D 394 *********************** 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 395 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 351 time to evaluate : 2.762 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 186 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7949 (mm) REVERT: D 460 ASP cc_start: 0.7601 (m-30) cc_final: 0.7367 (m-30) REVERT: D 823 PHE cc_start: 0.8245 (t80) cc_final: 0.7933 (t80) REVERT: I 819 ARG cc_start: 0.8393 (tpp-160) cc_final: 0.8067 (tpp80) REVERT: I 823 PHE cc_start: 0.8214 (t80) cc_final: 0.7921 (t80) REVERT: C 191 ARG cc_start: 0.8565 (ttm-80) cc_final: 0.7964 (tpt90) REVERT: C 323 ILE cc_start: 0.8420 (pt) cc_final: 0.7638 (mt) REVERT: C 614 PHE cc_start: 0.8344 (m-80) cc_final: 0.8114 (m-80) REVERT: C 821 GLU cc_start: 0.8623 (tp30) cc_final: 0.8079 (tp30) REVERT: C 824 TRP cc_start: 0.7693 (t60) cc_final: 0.7270 (t60) REVERT: C 920 HIS cc_start: 0.7092 (OUTLIER) cc_final: 0.6065 (t-170) outliers start: 44 outliers final: 30 residues processed: 376 average time/residue: 0.6720 time to fit residues: 374.0849 Evaluate side-chains 350 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 318 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 514 ASP Chi-restraints excluded: chain D residue 632 ASN Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain I residue 278 LEU 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 775 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 813 SER 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 192 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 195 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 18056 Z= 0.365 Angle : 0.659 11.458 24583 Z= 0.342 Chirality : 0.070 1.456 2744 Planarity : 0.005 0.061 3051 Dihedral : 9.322 114.559 2809 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.33 % Favored : 94.48 % Rotamer: Outliers : 2.52 % Allowed : 14.06 % Favored : 83.41 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.18), residues: 2139 helix: 1.32 (0.15), residues: 1146 sheet: 0.59 (0.46), residues: 132 loop : -1.32 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 954 HIS 0.009 0.002 HIS D 434 PHE 0.018 0.002 PHE D 187 TYR 0.024 0.002 TYR I 489 ARG 0.007 0.001 ARG D 689 *********************** 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 362 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 315 time to evaluate : 2.798 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 186 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8026 (mm) REVERT: D 882 LEU cc_start: 0.8163 (tp) cc_final: 0.7951 (tp) REVERT: I 819 ARG cc_start: 0.8414 (tpp-160) cc_final: 0.8101 (tpp80) REVERT: I 823 PHE cc_start: 0.8307 (t80) cc_final: 0.8104 (t80) REVERT: I 837 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: C 188 PHE cc_start: 0.8318 (m-80) cc_final: 0.7986 (m-10) REVERT: C 191 ARG cc_start: 0.8588 (ttm-80) cc_final: 0.8356 (mtp85) REVERT: C 306 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6616 (mm-30) outliers start: 47 outliers final: 35 residues processed: 344 average time/residue: 0.6838 time to fit residues: 348.9111 Evaluate side-chains 344 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 307 time to evaluate : 2.888 ------------------------------------------------------------------------------- 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 307 THR Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 632 ASN Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 341 ASP Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 424 SER Chi-restraints excluded: chain I residue 459 LEU Chi-restraints excluded: chain I residue 510 ILE 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 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 486 ASP 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 820 ASN Chi-restraints excluded: chain C residue 879 THR Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 154 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 185 optimal weight: 0.0050 chunk 52 optimal weight: 5.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 822 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18056 Z= 0.174 Angle : 0.594 11.387 24583 Z= 0.304 Chirality : 0.069 1.435 2744 Planarity : 0.005 0.065 3051 Dihedral : 8.727 117.330 2809 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.63 % Favored : 95.18 % Rotamer: Outliers : 1.83 % Allowed : 14.81 % Favored : 83.36 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2139 helix: 1.61 (0.16), residues: 1147 sheet: 0.39 (0.44), residues: 141 loop : -1.19 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 954 HIS 0.006 0.001 HIS D 920 PHE 0.018 0.001 PHE D 187 TYR 0.017 0.001 TYR I 489 ARG 0.008 0.000 ARG I 394 *********************** 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 354 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 320 time to evaluate : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 186 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7979 (mm) REVERT: I 323 ILE cc_start: 0.8374 (pt) cc_final: 0.7521 (mt) REVERT: I 819 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8095 (tpp80) REVERT: I 837 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: C 188 PHE cc_start: 0.8313 (m-80) cc_final: 0.7987 (m-10) REVERT: C 323 ILE cc_start: 0.8442 (pt) cc_final: 0.7703 (mt) REVERT: C 820 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8910 (t0) outliers start: 34 outliers final: 27 residues processed: 338 average time/residue: 0.7068 time to fit residues: 355.9224 Evaluate side-chains 333 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 303 time to evaluate : 2.836 ------------------------------------------------------------------------------- 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 665 GLU Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain I residue 399 MET 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 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 820 ASN Chi-restraints excluded: chain C residue 879 THR Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 108 optimal weight: 0.0770 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18056 Z= 0.181 Angle : 0.589 11.370 24583 Z= 0.301 Chirality : 0.069 1.430 2744 Planarity : 0.004 0.056 3051 Dihedral : 8.041 114.846 2809 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.24 % Favored : 94.58 % Rotamer: Outliers : 1.83 % Allowed : 15.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 2139 helix: 1.70 (0.16), residues: 1155 sheet: 0.37 (0.44), residues: 141 loop : -1.11 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 954 HIS 0.005 0.001 HIS D 434 PHE 0.032 0.001 PHE I 913 TYR 0.014 0.001 TYR I 489 ARG 0.005 0.000 ARG D 394 *********************** 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 351 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 317 time to evaluate : 2.819 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: D 186 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7991 (mm) REVERT: D 188 PHE cc_start: 0.8186 (m-80) cc_final: 0.7910 (m-80) REVERT: I 323 ILE cc_start: 0.8365 (pt) cc_final: 0.7486 (mt) REVERT: I 819 ARG cc_start: 0.8402 (tpp-160) cc_final: 0.8087 (tpp80) REVERT: I 837 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: C 188 PHE cc_start: 0.8285 (m-80) cc_final: 0.7986 (m-10) REVERT: C 191 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.7948 (tpt90) REVERT: C 323 ILE cc_start: 0.8443 (pt) cc_final: 0.7715 (mt) REVERT: C 820 ASN cc_start: 0.9126 (OUTLIER) cc_final: 0.8913 (t0) REVERT: C 921 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8385 (tt) outliers start: 34 outliers final: 26 residues processed: 337 average time/residue: 0.7221 time to fit residues: 366.1517 Evaluate side-chains 334 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 304 time to evaluate : 3.201 ------------------------------------------------------------------------------- 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 407 THR Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain I residue 222 PHE Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 459 LEU 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 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 683 MET Chi-restraints excluded: chain C residue 714 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 879 THR Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 151 optimal weight: 0.0870 chunk 174 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18056 Z= 0.176 Angle : 0.577 11.848 24583 Z= 0.297 Chirality : 0.069 1.431 2744 Planarity : 0.004 0.059 3051 Dihedral : 7.255 113.339 2805 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.10 % Favored : 94.72 % Rotamer: Outliers : 1.77 % Allowed : 15.73 % Favored : 82.50 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 2139 helix: 1.76 (0.16), residues: 1157 sheet: 0.59 (0.46), residues: 131 loop : -1.05 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 954 HIS 0.005 0.001 HIS D 434 PHE 0.019 0.001 PHE I 913 TYR 0.014 0.001 TYR D 756 ARG 0.009 0.000 ARG C 243 *********************** 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 350 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 317 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 186 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7968 (mm) REVERT: D 188 PHE cc_start: 0.8132 (m-80) cc_final: 0.7869 (m-80) REVERT: I 323 ILE cc_start: 0.8370 (pt) cc_final: 0.7447 (mt) REVERT: I 819 ARG cc_start: 0.8396 (tpp-160) cc_final: 0.8083 (tpp80) REVERT: C 188 PHE cc_start: 0.8255 (m-80) cc_final: 0.7973 (m-10) REVERT: C 191 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.7929 (tpt90) REVERT: C 323 ILE cc_start: 0.8452 (pt) cc_final: 0.7699 (mt) REVERT: C 820 ASN cc_start: 0.9126 (OUTLIER) cc_final: 0.8917 (t0) outliers start: 33 outliers final: 25 residues processed: 335 average time/residue: 0.6781 time to fit residues: 338.7464 Evaluate side-chains 335 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 308 time to evaluate : 2.742 ------------------------------------------------------------------------------- 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 407 THR Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain D residue 921 LEU Chi-restraints excluded: chain I residue 222 PHE Chi-restraints excluded: chain I residue 399 MET 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 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 683 MET Chi-restraints excluded: chain C residue 714 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 879 THR Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 131 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18056 Z= 0.241 Angle : 0.593 11.377 24583 Z= 0.305 Chirality : 0.069 1.437 2744 Planarity : 0.005 0.094 3051 Dihedral : 6.766 113.074 2805 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.47 % Favored : 94.34 % Rotamer: Outliers : 1.61 % Allowed : 16.37 % Favored : 82.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 2139 helix: 1.77 (0.16), residues: 1155 sheet: 0.21 (0.45), residues: 141 loop : -1.10 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 954 HIS 0.007 0.001 HIS D 434 PHE 0.021 0.001 PHE I 913 TYR 0.011 0.001 TYR I 489 ARG 0.008 0.000 ARG I 243 *********************** 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 350 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 320 time to evaluate : 2.719 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: D 186 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7966 (mm) REVERT: D 188 PHE cc_start: 0.8119 (m-80) cc_final: 0.7874 (m-80) REVERT: I 819 ARG cc_start: 0.8409 (tpp-160) cc_final: 0.8087 (tpp80) REVERT: C 188 PHE cc_start: 0.8239 (m-80) cc_final: 0.7951 (m-10) REVERT: C 191 ARG cc_start: 0.8530 (ttm-80) cc_final: 0.7938 (tpt90) REVERT: C 306 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6590 (mm-30) REVERT: C 820 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8916 (t0) outliers start: 30 outliers final: 24 residues processed: 337 average time/residue: 0.6881 time to fit residues: 346.0649 Evaluate side-chains 336 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 310 time to evaluate : 3.107 ------------------------------------------------------------------------------- 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 632 ASN Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain I residue 222 PHE Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 510 ILE Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain I residue 784 LEU Chi-restraints excluded: chain I residue 820 ASN Chi-restraints excluded: chain I residue 879 THR 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 683 MET Chi-restraints excluded: chain C residue 714 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 879 THR Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 191 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18056 Z= 0.211 Angle : 0.586 11.370 24583 Z= 0.303 Chirality : 0.069 1.431 2744 Planarity : 0.005 0.086 3051 Dihedral : 6.649 113.666 2805 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.61 % Favored : 94.20 % Rotamer: Outliers : 1.40 % Allowed : 16.59 % Favored : 82.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 2139 helix: 1.79 (0.16), residues: 1155 sheet: 0.17 (0.45), residues: 141 loop : -1.07 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 954 HIS 0.006 0.001 HIS D 434 PHE 0.018 0.001 PHE I 913 TYR 0.012 0.001 TYR I 756 ARG 0.010 0.000 ARG C 394 *********************** 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 348 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 322 time to evaluate : 2.755 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 186 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7966 (mm) REVERT: D 188 PHE cc_start: 0.8091 (m-80) cc_final: 0.7855 (m-80) REVERT: D 523 ILE cc_start: 0.8896 (mp) cc_final: 0.8542 (mp) REVERT: I 323 ILE cc_start: 0.8424 (pt) cc_final: 0.7452 (mt) REVERT: I 819 ARG cc_start: 0.8401 (tpp-160) cc_final: 0.8077 (tpp80) REVERT: C 191 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.7923 (tpt90) REVERT: C 323 ILE cc_start: 0.8411 (pt) cc_final: 0.7690 (mt) REVERT: C 820 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8904 (t0) outliers start: 26 outliers final: 23 residues processed: 336 average time/residue: 0.6769 time to fit residues: 340.6330 Evaluate side-chains 332 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 307 time to evaluate : 2.740 ------------------------------------------------------------------------------- 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 632 ASN Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain I residue 222 PHE Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 510 ILE Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain I residue 784 LEU Chi-restraints excluded: chain I residue 820 ASN Chi-restraints excluded: chain I residue 879 THR 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 683 MET Chi-restraints excluded: chain C residue 714 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 879 THR Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 141 optimal weight: 0.0870 chunk 213 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18056 Z= 0.244 Angle : 0.598 11.385 24583 Z= 0.309 Chirality : 0.069 1.436 2744 Planarity : 0.005 0.081 3051 Dihedral : 6.606 113.854 2805 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.66 % Favored : 94.16 % Rotamer: Outliers : 1.45 % Allowed : 17.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 2139 helix: 1.74 (0.16), residues: 1157 sheet: 0.33 (0.47), residues: 131 loop : -1.09 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 954 HIS 0.006 0.001 HIS D 434 PHE 0.025 0.001 PHE I 913 TYR 0.015 0.001 TYR D 505 ARG 0.011 0.000 ARG D 394 ********************** 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 340 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 313 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 188 PHE cc_start: 0.8098 (m-80) cc_final: 0.7866 (m-80) REVERT: I 770 PRO cc_start: 0.6946 (Cg_exo) cc_final: 0.6726 (Cg_endo) REVERT: I 819 ARG cc_start: 0.8383 (tpp-160) cc_final: 0.8055 (tpp80) REVERT: C 820 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8917 (t0) outliers start: 27 outliers final: 24 residues processed: 326 average time/residue: 0.6612 time to fit residues: 320.9295 Evaluate side-chains 330 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 305 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 632 ASN Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 813 SER Chi-restraints excluded: chain D residue 920 HIS Chi-restraints excluded: chain I residue 222 PHE Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 510 ILE Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain I residue 784 LEU Chi-restraints excluded: chain I residue 820 ASN Chi-restraints excluded: chain I residue 879 THR 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 683 MET Chi-restraints excluded: chain C residue 714 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 879 THR Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 463 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.170928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123009 restraints weight = 63909.793| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.05 r_work: 0.3322 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18056 Z= 0.258 Angle : 0.601 11.417 24583 Z= 0.312 Chirality : 0.069 1.445 2744 Planarity : 0.005 0.112 3051 Dihedral : 6.626 114.291 2805 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.12 % Favored : 93.78 % Rotamer: Outliers : 1.66 % Allowed : 16.80 % Favored : 81.54 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2139 helix: 1.70 (0.15), residues: 1156 sheet: 0.49 (0.48), residues: 121 loop : -1.11 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 217 HIS 0.006 0.001 HIS D 434 PHE 0.029 0.001 PHE I 913 TYR 0.014 0.001 TYR D 528 ARG 0.015 0.001 ARG I 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8888.86 seconds wall clock time: 158 minutes 9.99 seconds (9489.99 seconds total)