Starting phenix.real_space_refine on Sat Feb 17 05:29:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d5k_30583/02_2024/7d5k_30583.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d5k_30583/02_2024/7d5k_30583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d5k_30583/02_2024/7d5k_30583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d5k_30583/02_2024/7d5k_30583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d5k_30583/02_2024/7d5k_30583.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d5k_30583/02_2024/7d5k_30583.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 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: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 11559 2.51 5 N 2928 2.21 5 O 3078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ASP 334": "OD1" <-> "OD2" Residue "A ASP 361": "OD1" <-> "OD2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ASP 464": "OD1" <-> "OD2" Residue "A ASP 475": "OD1" <-> "OD2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ASP 334": "OD1" <-> "OD2" Residue "B ASP 361": "OD1" <-> "OD2" Residue "B ASP 365": "OD1" <-> "OD2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B ASP 464": "OD1" <-> "OD2" Residue "B ASP 475": "OD1" <-> "OD2" Residue "B GLU 493": "OE1" <-> "OE2" Residue "B PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "B PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ASP 334": "OD1" <-> "OD2" Residue "C ASP 361": "OD1" <-> "OD2" Residue "C ASP 365": "OD1" <-> "OD2" Residue "C PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 432": "NH1" <-> "NH2" Residue "C ASP 464": "OD1" <-> "OD2" Residue "C ASP 475": "OD1" <-> "OD2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 731": "OE1" <-> "OE2" Residue "C PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17667 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5843 Classifications: {'peptide': 727} Link IDs: {'PTRANS': 47, 'TRANS': 679} Chain breaks: 2 Chain: "B" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5843 Classifications: {'peptide': 727} Link IDs: {'PTRANS': 47, 'TRANS': 679} Chain breaks: 2 Chain: "C" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5843 Classifications: {'peptide': 727} Link IDs: {'PTRANS': 47, 'TRANS': 679} Chain breaks: 2 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.36, per 1000 atoms: 0.53 Number of scatterers: 17667 At special positions: 0 Unit cell: (136.962, 138.049, 109.787, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3078 8.00 N 2928 7.00 C 11559 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " BGC D 1 " - " BGC D 2 " " BGC E 1 " - " BGC E 2 " " BGC F 1 " - " BGC F 2 " " BGC G 1 " - " BGC G 2 " " BGC H 1 " - " BGC H 2 " " BGC I 1 " - " BGC I 2 " Time building additional restraints: 6.83 Conformation dependent library (CDL) restraints added in 3.3 seconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4068 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 9 sheets defined 57.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 250 through 274 Processing helix chain 'A' and resid 279 through 302 removed outlier: 4.149A pdb=" N TRP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 313 through 322 removed outlier: 3.649A pdb=" N LEU A 317 " --> pdb=" O TYR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 3.516A pdb=" N THR A 350 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 377 through 402 removed outlier: 3.904A pdb=" N PHE A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Proline residue: A 396 - end of helix Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 426 through 453 removed outlier: 4.086A pdb=" N ARG A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 531 removed outlier: 3.839A pdb=" N VAL A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 removed outlier: 3.906A pdb=" N CYS A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 595 removed outlier: 3.589A pdb=" N PHE A 593 " --> pdb=" O ASN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 601 Processing helix chain 'A' and resid 617 through 621 removed outlier: 3.580A pdb=" N TYR A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 621' Processing helix chain 'A' and resid 676 through 684 removed outlier: 3.881A pdb=" N PHE A 680 " --> pdb=" O SER A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 706 through 718 removed outlier: 3.699A pdb=" N LEU A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 751 removed outlier: 3.811A pdb=" N MET A 749 " --> pdb=" O THR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 792 Processing helix chain 'A' and resid 809 through 822 Processing helix chain 'A' and resid 825 through 841 removed outlier: 3.560A pdb=" N LEU A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA A 831 " --> pdb=" O LEU A 827 " (cutoff:3.500A) Proline residue: A 836 - end of helix Processing helix chain 'A' and resid 853 through 877 removed outlier: 4.218A pdb=" N PHE A 857 " --> pdb=" O PHE A 853 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 862 " --> pdb=" O PHE A 858 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 895 removed outlier: 4.149A pdb=" N VAL A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 912 Processing helix chain 'A' and resid 938 through 940 No H-bonds generated for 'chain 'A' and resid 938 through 940' Processing helix chain 'A' and resid 941 through 965 removed outlier: 3.590A pdb=" N THR A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 996 removed outlier: 4.195A pdb=" N LYS A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) Proline residue: A 989 - end of helix Processing helix chain 'A' and resid 1004 through 1024 Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'B' and resid 250 through 274 Processing helix chain 'B' and resid 279 through 302 removed outlier: 4.148A pdb=" N TRP B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 313 through 322 removed outlier: 3.649A pdb=" N LEU B 317 " --> pdb=" O TYR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.517A pdb=" N THR B 350 " --> pdb=" O PRO B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 366 Processing helix chain 'B' and resid 377 through 402 removed outlier: 3.904A pdb=" N PHE B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 426 through 453 removed outlier: 4.086A pdb=" N ARG B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 531 removed outlier: 3.840A pdb=" N VAL B 529 " --> pdb=" O ARG B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 removed outlier: 3.906A pdb=" N CYS B 556 " --> pdb=" O ARG B 552 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE B 557 " --> pdb=" O GLU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.590A pdb=" N PHE B 593 " --> pdb=" O ASN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 601 Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.580A pdb=" N TYR B 621 " --> pdb=" O ARG B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 617 through 621' Processing helix chain 'B' and resid 676 through 684 removed outlier: 3.881A pdb=" N PHE B 680 " --> pdb=" O SER B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 Processing helix chain 'B' and resid 706 through 718 removed outlier: 3.698A pdb=" N LEU B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS B 716 " --> pdb=" O LYS B 712 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 751 removed outlier: 3.811A pdb=" N MET B 749 " --> pdb=" O THR B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 792 Processing helix chain 'B' and resid 809 through 822 Processing helix chain 'B' and resid 825 through 841 removed outlier: 3.561A pdb=" N LEU B 830 " --> pdb=" O SER B 826 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 831 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Proline residue: B 836 - end of helix Processing helix chain 'B' and resid 853 through 877 removed outlier: 4.218A pdb=" N PHE B 857 " --> pdb=" O PHE B 853 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE B 862 " --> pdb=" O PHE B 858 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 895 removed outlier: 4.150A pdb=" N VAL B 891 " --> pdb=" O GLU B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 912 Processing helix chain 'B' and resid 938 through 940 No H-bonds generated for 'chain 'B' and resid 938 through 940' Processing helix chain 'B' and resid 941 through 965 removed outlier: 3.590A pdb=" N THR B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 996 removed outlier: 4.194A pdb=" N LYS B 976 " --> pdb=" O PRO B 972 " (cutoff:3.500A) Proline residue: B 989 - end of helix Processing helix chain 'B' and resid 1004 through 1024 Processing helix chain 'C' and resid 246 through 249 Processing helix chain 'C' and resid 250 through 274 Processing helix chain 'C' and resid 279 through 302 removed outlier: 4.148A pdb=" N TRP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 313 through 322 removed outlier: 3.648A pdb=" N LEU C 317 " --> pdb=" O TYR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 359 removed outlier: 3.516A pdb=" N THR C 350 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 366 Processing helix chain 'C' and resid 377 through 402 removed outlier: 3.905A pdb=" N PHE C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU C 389 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Proline residue: C 396 - end of helix Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 426 through 453 removed outlier: 4.086A pdb=" N ARG C 436 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 531 removed outlier: 3.840A pdb=" N VAL C 529 " --> pdb=" O ARG C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 559 removed outlier: 3.907A pdb=" N CYS C 556 " --> pdb=" O ARG C 552 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE C 557 " --> pdb=" O GLU C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 595 removed outlier: 3.591A pdb=" N PHE C 593 " --> pdb=" O ASN C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 601 Processing helix chain 'C' and resid 617 through 621 removed outlier: 3.580A pdb=" N TYR C 621 " --> pdb=" O ARG C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 617 through 621' Processing helix chain 'C' and resid 676 through 684 removed outlier: 3.880A pdb=" N PHE C 680 " --> pdb=" O SER C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 695 Processing helix chain 'C' and resid 706 through 718 removed outlier: 3.698A pdb=" N LEU C 710 " --> pdb=" O SER C 706 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS C 716 " --> pdb=" O LYS C 712 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 751 removed outlier: 3.812A pdb=" N MET C 749 " --> pdb=" O THR C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 792 Processing helix chain 'C' and resid 809 through 822 Processing helix chain 'C' and resid 825 through 841 removed outlier: 3.560A pdb=" N LEU C 830 " --> pdb=" O SER C 826 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C 831 " --> pdb=" O LEU C 827 " (cutoff:3.500A) Proline residue: C 836 - end of helix Processing helix chain 'C' and resid 853 through 877 removed outlier: 4.217A pdb=" N PHE C 857 " --> pdb=" O PHE C 853 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 862 " --> pdb=" O PHE C 858 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 895 removed outlier: 4.149A pdb=" N VAL C 891 " --> pdb=" O GLU C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 912 Processing helix chain 'C' and resid 938 through 940 No H-bonds generated for 'chain 'C' and resid 938 through 940' Processing helix chain 'C' and resid 941 through 965 removed outlier: 3.590A pdb=" N THR C 945 " --> pdb=" O LEU C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 996 removed outlier: 4.194A pdb=" N LYS C 976 " --> pdb=" O PRO C 972 " (cutoff:3.500A) Proline residue: C 989 - end of helix Processing helix chain 'C' and resid 1004 through 1024 Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 244 Processing sheet with id=AA2, first strand: chain 'A' and resid 479 through 483 removed outlier: 6.160A pdb=" N CYS A 369 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A 503 " --> pdb=" O CYS A 369 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE A 371 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 333 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N TYR A 370 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE A 335 " --> pdb=" O TYR A 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER A 372 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 337 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASP A 334 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU A 539 " --> pdb=" O ASP A 334 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE A 336 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS A 613 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS A 568 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE A 757 " --> pdb=" O CYS A 568 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 570 " --> pdb=" O ILE A 757 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 543 through 545 removed outlier: 6.524A pdb=" N ARG A 575 " --> pdb=" O GLY A 768 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 240 through 244 Processing sheet with id=AA5, first strand: chain 'B' and resid 479 through 483 removed outlier: 6.160A pdb=" N CYS B 369 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL B 503 " --> pdb=" O CYS B 369 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE B 371 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B 333 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N TYR B 370 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE B 335 " --> pdb=" O TYR B 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER B 372 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 337 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASP B 334 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU B 539 " --> pdb=" O ASP B 334 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE B 336 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYS B 613 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS B 568 " --> pdb=" O ARG B 616 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE B 757 " --> pdb=" O CYS B 568 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 570 " --> pdb=" O ILE B 757 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 543 through 545 removed outlier: 6.524A pdb=" N ARG B 575 " --> pdb=" O GLY B 768 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 240 through 244 Processing sheet with id=AA8, first strand: chain 'C' and resid 479 through 483 removed outlier: 6.159A pdb=" N CYS C 369 " --> pdb=" O VAL C 501 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL C 503 " --> pdb=" O CYS C 369 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE C 371 " --> pdb=" O VAL C 503 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL C 333 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N TYR C 370 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE C 335 " --> pdb=" O TYR C 370 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER C 372 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 337 " --> pdb=" O SER C 372 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASP C 334 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU C 539 " --> pdb=" O ASP C 334 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE C 336 " --> pdb=" O LEU C 539 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYS C 613 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS C 568 " --> pdb=" O ARG C 616 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE C 757 " --> pdb=" O CYS C 568 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL C 570 " --> pdb=" O ILE C 757 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 543 through 545 removed outlier: 6.523A pdb=" N ARG C 575 " --> pdb=" O GLY C 768 " (cutoff:3.500A) 854 hydrogen bonds defined for protein. 2535 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: 5.19 Time building geometry restraints manager: 7.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4240 1.33 - 1.45: 3918 1.45 - 1.57: 9863 1.57 - 1.69: 0 1.69 - 1.81: 165 Bond restraints: 18186 Sorted by residual: bond pdb=" C5 BGC H 2 " pdb=" O5 BGC H 2 " ideal model delta sigma weight residual 1.411 1.437 -0.026 2.00e-02 2.50e+03 1.64e+00 bond pdb=" C5 BGC G 1 " pdb=" O5 BGC G 1 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" C5 BGC E 2 " pdb=" O5 BGC E 2 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" C5 BGC I 2 " pdb=" O5 BGC I 2 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" C5 BGC F 2 " pdb=" O5 BGC F 2 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.58e+00 ... (remaining 18181 not shown) Histogram of bond angle deviations from ideal: 99.82 - 106.65: 724 106.65 - 113.49: 9747 113.49 - 120.32: 6725 120.32 - 127.16: 7222 127.16 - 133.99: 299 Bond angle restraints: 24717 Sorted by residual: angle pdb=" CA LYS A 682 " pdb=" CB LYS A 682 " pdb=" CG LYS A 682 " ideal model delta sigma weight residual 114.10 108.27 5.83 2.00e+00 2.50e-01 8.49e+00 angle pdb=" CA LYS C 682 " pdb=" CB LYS C 682 " pdb=" CG LYS C 682 " ideal model delta sigma weight residual 114.10 108.30 5.80 2.00e+00 2.50e-01 8.40e+00 angle pdb=" CA LYS B 682 " pdb=" CB LYS B 682 " pdb=" CG LYS B 682 " ideal model delta sigma weight residual 114.10 108.32 5.78 2.00e+00 2.50e-01 8.37e+00 angle pdb=" NE ARG C 432 " pdb=" CZ ARG C 432 " pdb=" NH2 ARG C 432 " ideal model delta sigma weight residual 119.20 121.63 -2.43 9.00e-01 1.23e+00 7.31e+00 angle pdb=" NE ARG A 432 " pdb=" CZ ARG A 432 " pdb=" NH2 ARG A 432 " ideal model delta sigma weight residual 119.20 121.62 -2.42 9.00e-01 1.23e+00 7.22e+00 ... (remaining 24712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.83: 10169 21.83 - 43.66: 545 43.66 - 65.49: 107 65.49 - 87.32: 27 87.32 - 109.15: 24 Dihedral angle restraints: 10872 sinusoidal: 4554 harmonic: 6318 Sorted by residual: dihedral pdb=" C4 BGC E 1 " pdb=" C2 BGC E 1 " pdb=" C3 BGC E 1 " pdb=" O2 BGC E 1 " ideal model delta sinusoidal sigma weight residual 174.54 65.39 109.15 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C4 BGC I 1 " pdb=" C2 BGC I 1 " pdb=" C3 BGC I 1 " pdb=" O2 BGC I 1 " ideal model delta sinusoidal sigma weight residual 174.54 65.40 109.14 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C4 BGC G 1 " pdb=" C2 BGC G 1 " pdb=" C3 BGC G 1 " pdb=" O2 BGC G 1 " ideal model delta sinusoidal sigma weight residual 174.54 65.44 109.10 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 10869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2072 0.048 - 0.097: 538 0.097 - 0.145: 99 0.145 - 0.193: 15 0.193 - 0.241: 3 Chirality restraints: 2727 Sorted by residual: chirality pdb=" CB ILE C 367 " pdb=" CA ILE C 367 " pdb=" CG1 ILE C 367 " pdb=" CG2 ILE C 367 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE A 367 " pdb=" CA ILE A 367 " pdb=" CG1 ILE A 367 " pdb=" CG2 ILE A 367 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE B 367 " pdb=" CA ILE B 367 " pdb=" CG1 ILE B 367 " pdb=" CG2 ILE B 367 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2724 not shown) Planarity restraints: 3081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 306 " 0.013 2.00e-02 2.50e+03 1.48e-02 3.84e+00 pdb=" CG PHE B 306 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 306 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 306 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 306 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 306 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 306 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 306 " -0.012 2.00e-02 2.50e+03 1.47e-02 3.76e+00 pdb=" CG PHE C 306 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE C 306 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 306 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE C 306 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 306 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 306 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 306 " 0.012 2.00e-02 2.50e+03 1.45e-02 3.67e+00 pdb=" CG PHE A 306 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 306 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 306 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 306 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 306 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 306 " 0.002 2.00e-02 2.50e+03 ... (remaining 3078 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 177 2.68 - 3.23: 17442 3.23 - 3.79: 26599 3.79 - 4.34: 35443 4.34 - 4.90: 57359 Nonbonded interactions: 137020 Sorted by model distance: nonbonded pdb=" O ALA C 331 " pdb=" OH TYR C 362 " model vdw 2.124 2.440 nonbonded pdb=" O ALA B 331 " pdb=" OH TYR B 362 " model vdw 2.124 2.440 nonbonded pdb=" O ALA A 331 " pdb=" OH TYR A 362 " model vdw 2.125 2.440 nonbonded pdb=" OE1 GLU A 723 " pdb=" OH TYR A 736 " model vdw 2.193 2.440 nonbonded pdb=" OE1 GLU B 723 " pdb=" OH TYR B 736 " model vdw 2.193 2.440 ... (remaining 137015 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 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.560 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 45.270 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 : 0.003 0.030 18186 Z= 0.212 Angle : 0.691 7.960 24717 Z= 0.365 Chirality : 0.044 0.241 2727 Planarity : 0.005 0.058 3081 Dihedral : 15.383 109.149 6804 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.79 % Allowed : 1.43 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.18), residues: 2163 helix: 0.90 (0.15), residues: 1167 sheet: -1.15 (0.38), residues: 147 loop : -1.21 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 800 HIS 0.003 0.001 HIS A 986 PHE 0.034 0.001 PHE B 306 TYR 0.020 0.002 TYR B 758 ARG 0.006 0.001 ARG C 795 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 330 time to evaluate : 1.785 Fit side-chains REVERT: A 237 GLN cc_start: 0.7938 (mp10) cc_final: 0.7581 (mp10) REVERT: A 241 ARG cc_start: 0.7155 (ttp-110) cc_final: 0.6884 (ttm110) REVERT: A 360 MET cc_start: 0.8296 (ttp) cc_final: 0.7985 (ttp) REVERT: A 434 MET cc_start: 0.8289 (tpp) cc_final: 0.8002 (tpp) REVERT: A 908 LYS cc_start: 0.7816 (ttpt) cc_final: 0.6755 (ttpt) REVERT: B 237 GLN cc_start: 0.7931 (mp10) cc_final: 0.7305 (mp10) REVERT: B 343 MET cc_start: 0.7835 (mmm) cc_final: 0.7563 (mmm) REVERT: B 389 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7395 (mm-30) REVERT: B 474 LYS cc_start: 0.7779 (mttp) cc_final: 0.7483 (mmmm) REVERT: B 555 MET cc_start: 0.8951 (mmt) cc_final: 0.8712 (mmm) REVERT: B 786 LEU cc_start: 0.8392 (tp) cc_final: 0.8119 (tp) REVERT: B 847 MET cc_start: 0.9007 (pmm) cc_final: 0.8315 (pmm) REVERT: C 237 GLN cc_start: 0.8099 (mp10) cc_final: 0.7808 (mp10) REVERT: C 313 TYR cc_start: 0.8073 (m-10) cc_final: 0.7475 (m-80) REVERT: C 323 ARG cc_start: 0.7563 (ptt180) cc_final: 0.7233 (ptt90) REVERT: C 474 LYS cc_start: 0.7801 (mttp) cc_final: 0.7565 (mmtp) REVERT: C 795 ARG cc_start: 0.7160 (ptt-90) cc_final: 0.6827 (ptt-90) outliers start: 15 outliers final: 3 residues processed: 335 average time/residue: 0.3204 time to fit residues: 157.7019 Evaluate side-chains 287 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 284 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 90 optimal weight: 0.0970 chunk 55 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 196 optimal weight: 0.0470 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18186 Z= 0.219 Angle : 0.615 7.957 24717 Z= 0.303 Chirality : 0.043 0.182 2727 Planarity : 0.004 0.042 3081 Dihedral : 9.776 92.006 2625 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.96 % Allowed : 6.77 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.18), residues: 2163 helix: 1.10 (0.15), residues: 1173 sheet: -1.12 (0.37), residues: 162 loop : -1.19 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 800 HIS 0.004 0.001 HIS B 514 PHE 0.027 0.001 PHE B 306 TYR 0.021 0.002 TYR C 758 ARG 0.006 0.000 ARG A 795 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 298 time to evaluate : 2.037 Fit side-chains REVERT: A 237 GLN cc_start: 0.7925 (mp10) cc_final: 0.7292 (mp10) REVERT: A 360 MET cc_start: 0.8379 (ttp) cc_final: 0.8044 (ttp) REVERT: A 389 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7578 (mm-30) REVERT: A 434 MET cc_start: 0.8459 (tpp) cc_final: 0.8189 (tpp) REVERT: A 493 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7649 (mm-30) REVERT: A 527 SER cc_start: 0.8981 (m) cc_final: 0.8733 (m) REVERT: B 343 MET cc_start: 0.7931 (mmm) cc_final: 0.7673 (mmm) REVERT: B 389 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7584 (mm-30) REVERT: B 493 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7536 (mm-30) REVERT: B 527 SER cc_start: 0.9046 (m) cc_final: 0.8798 (m) REVERT: B 555 MET cc_start: 0.9005 (mmt) cc_final: 0.8639 (mmm) REVERT: B 786 LEU cc_start: 0.8415 (tp) cc_final: 0.8190 (tp) REVERT: B 807 LYS cc_start: 0.7198 (mttt) cc_final: 0.6585 (mtpp) REVERT: C 237 GLN cc_start: 0.8179 (mp10) cc_final: 0.7747 (mp10) REVERT: C 313 TYR cc_start: 0.8120 (m-10) cc_final: 0.7596 (m-80) REVERT: C 323 ARG cc_start: 0.7516 (ptt180) cc_final: 0.7173 (ptt90) REVERT: C 474 LYS cc_start: 0.7829 (mttp) cc_final: 0.7606 (mmtp) REVERT: C 713 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7670 (tm-30) REVERT: C 783 ARG cc_start: 0.7257 (mtp-110) cc_final: 0.7023 (mtp-110) REVERT: C 795 ARG cc_start: 0.7166 (ptt-90) cc_final: 0.6803 (ptt-90) REVERT: C 847 MET cc_start: 0.8926 (pmm) cc_final: 0.8535 (pmm) REVERT: C 908 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7387 (tttm) outliers start: 37 outliers final: 34 residues processed: 308 average time/residue: 0.3253 time to fit residues: 148.8227 Evaluate side-chains 322 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 288 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 490 HIS Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 682 LYS Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 196 optimal weight: 0.3980 chunk 212 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 157 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS A 677 GLN ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN B 677 GLN ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18186 Z= 0.217 Angle : 0.602 7.864 24717 Z= 0.293 Chirality : 0.043 0.181 2727 Planarity : 0.004 0.035 3081 Dihedral : 6.450 48.356 2616 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.12 % Allowed : 10.05 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2163 helix: 1.27 (0.16), residues: 1179 sheet: -1.02 (0.38), residues: 162 loop : -1.20 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 800 HIS 0.004 0.001 HIS B 514 PHE 0.020 0.001 PHE B 306 TYR 0.019 0.002 TYR C 758 ARG 0.006 0.000 ARG A 795 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 303 time to evaluate : 1.863 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7954 (mp10) cc_final: 0.7542 (mp10) REVERT: A 255 MET cc_start: 0.7340 (mtm) cc_final: 0.7138 (mtm) REVERT: A 360 MET cc_start: 0.8459 (ttp) cc_final: 0.8186 (ttp) REVERT: A 389 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7655 (mm-30) REVERT: A 527 SER cc_start: 0.8951 (m) cc_final: 0.8719 (m) REVERT: A 886 ASN cc_start: 0.8322 (t0) cc_final: 0.7715 (t0) REVERT: B 237 GLN cc_start: 0.7984 (mp10) cc_final: 0.7572 (mp10) REVERT: B 389 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7610 (mm-30) REVERT: B 527 SER cc_start: 0.9103 (m) cc_final: 0.8869 (m) REVERT: B 555 MET cc_start: 0.9040 (mmt) cc_final: 0.8822 (mmm) REVERT: B 807 LYS cc_start: 0.7122 (mttt) cc_final: 0.6496 (mtpp) REVERT: C 237 GLN cc_start: 0.8133 (mp10) cc_final: 0.7699 (mp10) REVERT: C 403 ILE cc_start: 0.8182 (mm) cc_final: 0.7822 (mm) REVERT: C 474 LYS cc_start: 0.7811 (mttp) cc_final: 0.7599 (mmtp) REVERT: C 553 GLU cc_start: 0.7911 (tt0) cc_final: 0.7695 (tt0) REVERT: C 713 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7565 (tm-30) REVERT: C 786 LEU cc_start: 0.8322 (tp) cc_final: 0.8048 (tp) REVERT: C 795 ARG cc_start: 0.7157 (ptt-90) cc_final: 0.6867 (ptt-90) REVERT: C 847 MET cc_start: 0.8946 (pmm) cc_final: 0.8666 (pmm) outliers start: 40 outliers final: 31 residues processed: 315 average time/residue: 0.3174 time to fit residues: 149.8864 Evaluate side-chains 308 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 277 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 197 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18186 Z= 0.212 Angle : 0.587 7.470 24717 Z= 0.286 Chirality : 0.042 0.207 2727 Planarity : 0.004 0.035 3081 Dihedral : 5.527 46.495 2616 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.54 % Allowed : 10.79 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.18), residues: 2163 helix: 1.39 (0.16), residues: 1179 sheet: -0.80 (0.39), residues: 165 loop : -1.22 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 800 HIS 0.004 0.001 HIS A 514 PHE 0.013 0.001 PHE A 306 TYR 0.017 0.001 TYR A 758 ARG 0.006 0.000 ARG A 795 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 291 time to evaluate : 1.747 Fit side-chains REVERT: A 237 GLN cc_start: 0.7991 (mp10) cc_final: 0.7434 (mp10) REVERT: A 360 MET cc_start: 0.8438 (ttp) cc_final: 0.8155 (ttp) REVERT: A 373 ASP cc_start: 0.8379 (t0) cc_final: 0.8082 (t0) REVERT: A 389 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7599 (mm-30) REVERT: A 527 SER cc_start: 0.8875 (m) cc_final: 0.8649 (m) REVERT: A 675 MET cc_start: 0.6538 (tmm) cc_final: 0.6267 (tmm) REVERT: A 886 ASN cc_start: 0.8622 (t0) cc_final: 0.7947 (t0) REVERT: B 237 GLN cc_start: 0.8051 (mp10) cc_final: 0.7541 (mp10) REVERT: B 373 ASP cc_start: 0.8374 (t0) cc_final: 0.8156 (t0) REVERT: B 389 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7577 (mm-30) REVERT: B 527 SER cc_start: 0.9055 (m) cc_final: 0.8795 (m) REVERT: B 555 MET cc_start: 0.9035 (mmt) cc_final: 0.8829 (mmm) REVERT: B 807 LYS cc_start: 0.7197 (mttt) cc_final: 0.6585 (mtpp) REVERT: C 237 GLN cc_start: 0.8116 (mp10) cc_final: 0.7674 (pm20) REVERT: C 403 ILE cc_start: 0.8194 (mm) cc_final: 0.7837 (mm) REVERT: C 474 LYS cc_start: 0.7799 (mttp) cc_final: 0.7589 (mmtp) REVERT: C 553 GLU cc_start: 0.8002 (tt0) cc_final: 0.7767 (tt0) REVERT: C 752 ARG cc_start: 0.7254 (mtt180) cc_final: 0.7001 (mtt180) REVERT: C 795 ARG cc_start: 0.7246 (ptt-90) cc_final: 0.7027 (ptt-90) outliers start: 48 outliers final: 37 residues processed: 313 average time/residue: 0.3107 time to fit residues: 145.9099 Evaluate side-chains 315 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 278 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 718 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18186 Z= 0.214 Angle : 0.582 7.820 24717 Z= 0.283 Chirality : 0.042 0.257 2727 Planarity : 0.004 0.035 3081 Dihedral : 5.401 50.632 2616 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.65 % Allowed : 12.12 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2163 helix: 1.58 (0.16), residues: 1161 sheet: -0.82 (0.39), residues: 165 loop : -1.18 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 800 HIS 0.004 0.001 HIS A 514 PHE 0.011 0.001 PHE B 397 TYR 0.015 0.001 TYR A 758 ARG 0.005 0.000 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 296 time to evaluate : 1.989 Fit side-chains REVERT: A 237 GLN cc_start: 0.7970 (mp10) cc_final: 0.7587 (pm20) REVERT: A 311 GLU cc_start: 0.7832 (pt0) cc_final: 0.7576 (pt0) REVERT: A 360 MET cc_start: 0.8425 (ttp) cc_final: 0.8123 (ttp) REVERT: A 373 ASP cc_start: 0.8370 (t0) cc_final: 0.8025 (t0) REVERT: A 389 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7688 (mm-30) REVERT: A 527 SER cc_start: 0.8803 (m) cc_final: 0.8570 (m) REVERT: A 886 ASN cc_start: 0.8649 (t0) cc_final: 0.8085 (t0) REVERT: B 237 GLN cc_start: 0.8053 (mp10) cc_final: 0.7563 (mp10) REVERT: B 373 ASP cc_start: 0.8391 (t0) cc_final: 0.8035 (t0) REVERT: B 527 SER cc_start: 0.9010 (m) cc_final: 0.8783 (m) REVERT: B 555 MET cc_start: 0.9058 (mmt) cc_final: 0.8816 (mmm) REVERT: B 807 LYS cc_start: 0.7178 (mttt) cc_final: 0.6546 (mtpp) REVERT: C 237 GLN cc_start: 0.8109 (mp10) cc_final: 0.7736 (pm20) REVERT: C 403 ILE cc_start: 0.8208 (mm) cc_final: 0.7855 (mm) REVERT: C 474 LYS cc_start: 0.7792 (mttp) cc_final: 0.7575 (mmtp) REVERT: C 553 GLU cc_start: 0.7944 (tt0) cc_final: 0.7711 (tt0) REVERT: C 752 ARG cc_start: 0.7241 (mtt180) cc_final: 0.6994 (mtt180) REVERT: C 795 ARG cc_start: 0.7352 (ptt-90) cc_final: 0.7054 (ptt-90) outliers start: 50 outliers final: 40 residues processed: 317 average time/residue: 0.2942 time to fit residues: 140.5220 Evaluate side-chains 323 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 283 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 490 HIS Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 chunk 96 optimal weight: 0.0270 chunk 17 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18186 Z= 0.197 Angle : 0.574 7.896 24717 Z= 0.279 Chirality : 0.042 0.349 2727 Planarity : 0.004 0.034 3081 Dihedral : 5.236 57.179 2616 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.54 % Allowed : 12.54 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2163 helix: 1.66 (0.16), residues: 1161 sheet: -0.79 (0.39), residues: 165 loop : -1.15 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 800 HIS 0.004 0.001 HIS B 514 PHE 0.011 0.001 PHE B 397 TYR 0.015 0.001 TYR C 758 ARG 0.006 0.000 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 293 time to evaluate : 1.943 Fit side-chains REVERT: A 237 GLN cc_start: 0.7956 (mp10) cc_final: 0.7559 (pm20) REVERT: A 311 GLU cc_start: 0.7814 (pt0) cc_final: 0.7524 (pt0) REVERT: A 360 MET cc_start: 0.8414 (ttp) cc_final: 0.8127 (ttp) REVERT: A 373 ASP cc_start: 0.8256 (t0) cc_final: 0.7865 (t0) REVERT: A 389 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7665 (mm-30) REVERT: A 527 SER cc_start: 0.8778 (m) cc_final: 0.8557 (m) REVERT: A 757 ILE cc_start: 0.8839 (tt) cc_final: 0.8444 (mt) REVERT: A 784 TRP cc_start: 0.7896 (m-10) cc_final: 0.7408 (m-10) REVERT: A 886 ASN cc_start: 0.8664 (t0) cc_final: 0.8105 (t0) REVERT: B 237 GLN cc_start: 0.8050 (mp10) cc_final: 0.7583 (mp10) REVERT: B 373 ASP cc_start: 0.8359 (t0) cc_final: 0.7969 (t0) REVERT: B 527 SER cc_start: 0.8999 (m) cc_final: 0.8757 (m) REVERT: B 555 MET cc_start: 0.9051 (mmt) cc_final: 0.8816 (mmm) REVERT: B 807 LYS cc_start: 0.7212 (mttt) cc_final: 0.6572 (mtpp) REVERT: C 237 GLN cc_start: 0.8115 (mp10) cc_final: 0.7765 (pm20) REVERT: C 403 ILE cc_start: 0.8153 (mm) cc_final: 0.7793 (mm) REVERT: C 553 GLU cc_start: 0.7970 (tt0) cc_final: 0.7730 (tt0) REVERT: C 752 ARG cc_start: 0.7326 (mtt180) cc_final: 0.7068 (mtt180) REVERT: C 795 ARG cc_start: 0.7343 (ptt-90) cc_final: 0.7035 (ptt-90) outliers start: 48 outliers final: 43 residues processed: 317 average time/residue: 0.2947 time to fit residues: 140.2428 Evaluate side-chains 329 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 286 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 490 HIS Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 718 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 96 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18186 Z= 0.239 Angle : 0.595 9.272 24717 Z= 0.291 Chirality : 0.042 0.303 2727 Planarity : 0.004 0.034 3081 Dihedral : 5.051 59.226 2616 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.07 % Allowed : 13.07 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2163 helix: 1.70 (0.16), residues: 1161 sheet: -0.88 (0.38), residues: 165 loop : -1.17 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 800 HIS 0.004 0.001 HIS C 514 PHE 0.011 0.001 PHE B 397 TYR 0.017 0.002 TYR A 758 ARG 0.005 0.000 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 287 time to evaluate : 1.980 Fit side-chains REVERT: A 237 GLN cc_start: 0.7975 (mp10) cc_final: 0.7570 (pm20) REVERT: A 311 GLU cc_start: 0.7885 (pt0) cc_final: 0.7516 (pt0) REVERT: A 360 MET cc_start: 0.8445 (ttp) cc_final: 0.8188 (ttp) REVERT: A 373 ASP cc_start: 0.8286 (t0) cc_final: 0.7895 (t0) REVERT: A 389 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 527 SER cc_start: 0.8776 (m) cc_final: 0.8540 (m) REVERT: A 675 MET cc_start: 0.6730 (tmm) cc_final: 0.6425 (tmm) REVERT: A 757 ILE cc_start: 0.8889 (tt) cc_final: 0.8515 (mt) REVERT: A 886 ASN cc_start: 0.8689 (t0) cc_final: 0.7985 (t0) REVERT: B 237 GLN cc_start: 0.8062 (mp10) cc_final: 0.7575 (mp10) REVERT: B 255 MET cc_start: 0.7259 (mtm) cc_final: 0.7054 (mtm) REVERT: B 373 ASP cc_start: 0.8410 (t0) cc_final: 0.8016 (t0) REVERT: B 527 SER cc_start: 0.9008 (m) cc_final: 0.8761 (m) REVERT: B 555 MET cc_start: 0.9074 (mmt) cc_final: 0.8765 (mmm) REVERT: B 807 LYS cc_start: 0.7212 (mttt) cc_final: 0.6563 (mtpp) REVERT: B 847 MET cc_start: 0.8912 (pmm) cc_final: 0.8425 (pmm) REVERT: C 237 GLN cc_start: 0.8122 (mp10) cc_final: 0.7790 (pm20) REVERT: C 403 ILE cc_start: 0.8222 (mm) cc_final: 0.7874 (mm) REVERT: C 553 GLU cc_start: 0.8009 (tt0) cc_final: 0.7786 (tt0) REVERT: C 752 ARG cc_start: 0.7306 (mtt180) cc_final: 0.7054 (mtt180) REVERT: C 795 ARG cc_start: 0.7369 (ptt-90) cc_final: 0.7049 (ptt-90) REVERT: C 847 MET cc_start: 0.8834 (pmm) cc_final: 0.8462 (pmm) outliers start: 58 outliers final: 48 residues processed: 315 average time/residue: 0.3054 time to fit residues: 144.7619 Evaluate side-chains 327 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 279 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 490 HIS Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 718 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.9990 chunk 83 optimal weight: 0.0970 chunk 124 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 189 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18186 Z= 0.193 Angle : 0.578 9.426 24717 Z= 0.281 Chirality : 0.041 0.335 2727 Planarity : 0.004 0.034 3081 Dihedral : 4.623 48.812 2616 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.70 % Allowed : 13.86 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.18), residues: 2163 helix: 1.78 (0.16), residues: 1158 sheet: -0.79 (0.39), residues: 165 loop : -1.16 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 784 HIS 0.004 0.001 HIS B 514 PHE 0.012 0.001 PHE B 397 TYR 0.015 0.001 TYR C 758 ARG 0.008 0.000 ARG A 795 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 285 time to evaluate : 1.932 Fit side-chains REVERT: A 237 GLN cc_start: 0.7953 (mp10) cc_final: 0.7595 (pm20) REVERT: A 360 MET cc_start: 0.8385 (ttp) cc_final: 0.8078 (ttp) REVERT: A 373 ASP cc_start: 0.8217 (t0) cc_final: 0.7789 (t0) REVERT: A 386 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6767 (tp30) REVERT: A 389 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7712 (mm-30) REVERT: A 527 SER cc_start: 0.8744 (m) cc_final: 0.8525 (m) REVERT: A 675 MET cc_start: 0.6747 (tmm) cc_final: 0.6484 (tmm) REVERT: A 757 ILE cc_start: 0.8864 (tt) cc_final: 0.8506 (mt) REVERT: A 886 ASN cc_start: 0.8577 (t0) cc_final: 0.7890 (t0) REVERT: B 237 GLN cc_start: 0.8021 (mp10) cc_final: 0.7578 (mp10) REVERT: B 255 MET cc_start: 0.7258 (mtm) cc_final: 0.7039 (mtm) REVERT: B 373 ASP cc_start: 0.8345 (t0) cc_final: 0.7915 (t0) REVERT: B 527 SER cc_start: 0.9000 (m) cc_final: 0.8764 (m) REVERT: B 555 MET cc_start: 0.9068 (mmt) cc_final: 0.8801 (mmm) REVERT: B 847 MET cc_start: 0.8909 (pmm) cc_final: 0.8398 (pmm) REVERT: C 237 GLN cc_start: 0.7952 (mp10) cc_final: 0.7612 (pm20) REVERT: C 403 ILE cc_start: 0.8188 (mm) cc_final: 0.7823 (mm) REVERT: C 553 GLU cc_start: 0.7981 (tt0) cc_final: 0.7741 (tt0) REVERT: C 795 ARG cc_start: 0.7363 (ptt-90) cc_final: 0.7036 (ptt-90) REVERT: C 847 MET cc_start: 0.8848 (pmm) cc_final: 0.8585 (pmm) outliers start: 51 outliers final: 46 residues processed: 312 average time/residue: 0.3001 time to fit residues: 140.8259 Evaluate side-chains 331 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 285 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 490 HIS Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 718 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 59 optimal weight: 0.0970 chunk 175 optimal weight: 1.9990 chunk 183 optimal weight: 0.0870 chunk 193 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18186 Z= 0.275 Angle : 0.616 9.155 24717 Z= 0.301 Chirality : 0.043 0.345 2727 Planarity : 0.004 0.034 3081 Dihedral : 4.605 36.184 2616 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.80 % Allowed : 13.76 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2163 helix: 1.72 (0.16), residues: 1158 sheet: -0.73 (0.42), residues: 135 loop : -1.21 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 800 HIS 0.005 0.001 HIS C 716 PHE 0.013 0.001 PHE A 483 TYR 0.018 0.002 TYR A 816 ARG 0.008 0.000 ARG A 795 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 285 time to evaluate : 2.023 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8004 (mp10) cc_final: 0.7638 (pm20) REVERT: A 311 GLU cc_start: 0.7947 (pt0) cc_final: 0.7634 (pt0) REVERT: A 360 MET cc_start: 0.8460 (ttp) cc_final: 0.8228 (ttp) REVERT: A 373 ASP cc_start: 0.8290 (t0) cc_final: 0.7850 (t0) REVERT: A 386 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6844 (tp30) REVERT: A 389 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7734 (mm-30) REVERT: A 527 SER cc_start: 0.8772 (m) cc_final: 0.8542 (m) REVERT: A 675 MET cc_start: 0.6707 (tmm) cc_final: 0.6435 (tmm) REVERT: A 886 ASN cc_start: 0.8530 (t0) cc_final: 0.7879 (t0) REVERT: B 237 GLN cc_start: 0.8080 (mp10) cc_final: 0.7645 (mp10) REVERT: B 255 MET cc_start: 0.7289 (mtm) cc_final: 0.7087 (mtm) REVERT: B 373 ASP cc_start: 0.8440 (t0) cc_final: 0.8038 (t0) REVERT: B 511 PHE cc_start: 0.7594 (m-80) cc_final: 0.7355 (m-80) REVERT: B 555 MET cc_start: 0.9088 (mmt) cc_final: 0.8784 (mmm) REVERT: B 807 LYS cc_start: 0.7228 (mttt) cc_final: 0.6572 (mtpp) REVERT: B 847 MET cc_start: 0.8967 (pmm) cc_final: 0.8412 (pmm) REVERT: C 237 GLN cc_start: 0.7972 (mp10) cc_final: 0.7641 (pm20) REVERT: C 386 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6752 (tp30) REVERT: C 553 GLU cc_start: 0.7996 (tt0) cc_final: 0.7737 (tt0) REVERT: C 795 ARG cc_start: 0.7442 (ptt-90) cc_final: 0.7123 (ptt-90) REVERT: C 847 MET cc_start: 0.8839 (pmm) cc_final: 0.8530 (pmm) outliers start: 53 outliers final: 50 residues processed: 313 average time/residue: 0.3190 time to fit residues: 150.8337 Evaluate side-chains 332 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 282 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 490 HIS Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 718 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 142 optimal weight: 0.4980 chunk 215 optimal weight: 30.0000 chunk 198 optimal weight: 0.0060 chunk 171 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 132 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS A 538 ASN ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 HIS ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18186 Z= 0.176 Angle : 0.584 9.809 24717 Z= 0.282 Chirality : 0.041 0.369 2727 Planarity : 0.004 0.036 3081 Dihedral : 4.172 26.004 2616 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.49 % Allowed : 14.13 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2163 helix: 1.85 (0.16), residues: 1158 sheet: -0.59 (0.42), residues: 135 loop : -1.14 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 784 HIS 0.003 0.001 HIS B 514 PHE 0.012 0.001 PHE B 397 TYR 0.018 0.001 TYR B 758 ARG 0.008 0.000 ARG A 795 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 289 time to evaluate : 2.039 Fit side-chains REVERT: A 237 GLN cc_start: 0.8002 (mp10) cc_final: 0.7653 (pm20) REVERT: A 311 GLU cc_start: 0.7890 (pt0) cc_final: 0.7576 (pt0) REVERT: A 360 MET cc_start: 0.8362 (ttp) cc_final: 0.8103 (ttp) REVERT: A 373 ASP cc_start: 0.8162 (t0) cc_final: 0.7714 (t0) REVERT: A 386 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6774 (tp30) REVERT: A 389 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7703 (mm-30) REVERT: A 527 SER cc_start: 0.8720 (m) cc_final: 0.8509 (m) REVERT: A 675 MET cc_start: 0.6634 (tmm) cc_final: 0.6365 (tmm) REVERT: A 784 TRP cc_start: 0.7979 (m-10) cc_final: 0.7608 (m-10) REVERT: A 886 ASN cc_start: 0.8533 (t0) cc_final: 0.7923 (t0) REVERT: B 237 GLN cc_start: 0.8022 (mp10) cc_final: 0.7610 (pm20) REVERT: B 313 TYR cc_start: 0.7917 (m-80) cc_final: 0.7711 (m-10) REVERT: B 373 ASP cc_start: 0.8276 (t0) cc_final: 0.7820 (t0) REVERT: B 527 SER cc_start: 0.8983 (m) cc_final: 0.8759 (m) REVERT: B 555 MET cc_start: 0.9045 (mmt) cc_final: 0.8745 (mmm) REVERT: B 807 LYS cc_start: 0.7203 (mttt) cc_final: 0.6583 (mtpp) REVERT: B 847 MET cc_start: 0.8973 (pmm) cc_final: 0.8397 (pmm) REVERT: C 343 MET cc_start: 0.8097 (mpp) cc_final: 0.7792 (mpp) REVERT: C 553 GLU cc_start: 0.7959 (tt0) cc_final: 0.7721 (tt0) REVERT: C 795 ARG cc_start: 0.7376 (ptt-90) cc_final: 0.7053 (ptt-90) REVERT: C 847 MET cc_start: 0.8846 (pmm) cc_final: 0.8578 (pmm) outliers start: 47 outliers final: 44 residues processed: 314 average time/residue: 0.3011 time to fit residues: 142.4948 Evaluate side-chains 328 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 284 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 490 HIS Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 684 PHE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 490 HIS Chi-restraints excluded: chain C residue 527 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 684 PHE Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 719 SER Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 891 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 158 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 171 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 176 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 HIS A 538 ASN ** A 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.188939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.140162 restraints weight = 21435.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.136098 restraints weight = 18252.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.137669 restraints weight = 21170.051| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 18186 Z= 0.202 Angle : 0.765 59.198 24717 Z= 0.420 Chirality : 0.042 0.367 2727 Planarity : 0.004 0.034 3081 Dihedral : 4.216 32.302 2616 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.59 % Allowed : 14.29 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2163 helix: 1.85 (0.16), residues: 1158 sheet: -0.64 (0.42), residues: 135 loop : -1.13 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 784 HIS 0.003 0.001 HIS B 514 PHE 0.012 0.001 PHE B 397 TYR 0.016 0.001 TYR B 758 ARG 0.018 0.000 ARG C 617 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3539.24 seconds wall clock time: 65 minutes 26.16 seconds (3926.16 seconds total)