Starting phenix.real_space_refine on Sun Nov 17 11:52:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cau_16534/11_2024/8cau_16534_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cau_16534/11_2024/8cau_16534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cau_16534/11_2024/8cau_16534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cau_16534/11_2024/8cau_16534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cau_16534/11_2024/8cau_16534_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cau_16534/11_2024/8cau_16534_trim.cif" } resolution = 3.4 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= 0.001 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 60 5.16 5 C 8695 2.51 5 N 2240 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13545 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "B" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "C" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "D" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "E" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "F" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "G" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "I" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "J" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 13.25, per 1000 atoms: 0.98 Number of scatterers: 13545 At special positions: 0 Unit cell: (92.02, 92.88, 118.68, 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 60 16.00 O 2550 8.00 N 2240 7.00 C 8695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 501 " - " ASN A 23 " " NAG A 502 " - " ASN A 67 " " NAG B 501 " - " ASN B 23 " " NAG B 502 " - " ASN B 67 " " NAG C 501 " - " ASN C 23 " " NAG C 502 " - " ASN C 67 " " NAG D 501 " - " ASN D 23 " " NAG D 502 " - " ASN D 67 " " NAG E 501 " - " ASN E 23 " " NAG E 502 " - " ASN E 67 " " NAG P 1 " - " ASN A 110 " " NAG Q 1 " - " ASN B 110 " " NAG R 1 " - " ASN C 110 " " NAG S 1 " - " ASN D 110 " " NAG T 1 " - " ASN E 110 " Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 2.7 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3030 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 39 sheets defined 4.5% alpha, 48.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.796A pdb=" N LYS A 5 " --> pdb=" O GLU A 1 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 7 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 10 removed outlier: 3.550A pdb=" N TYR B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 8 " --> pdb=" O ARG B 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 4.170A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.512A pdb=" N TYR D 7 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 8 " --> pdb=" O ARG D 4 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'F' and resid 29 through 33 removed outlier: 4.015A pdb=" N TYR F 33 " --> pdb=" O PHE F 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 33 removed outlier: 4.041A pdb=" N TYR G 33 " --> pdb=" O PHE G 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 33 removed outlier: 4.023A pdb=" N TYR H 33 " --> pdb=" O PHE H 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 33 removed outlier: 4.023A pdb=" N TYR I 33 " --> pdb=" O PHE I 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 33 removed outlier: 3.997A pdb=" N TYR J 33 " --> pdb=" O PHE J 30 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 117 Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 117 removed outlier: 7.291A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR A 29 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 30 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.605A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.605A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 125 removed outlier: 3.534A pdb=" N LEU B 49 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL B 48 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 30 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 79 Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.586A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.586A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 114 through 117 removed outlier: 3.543A pdb=" N TRP C 59 " --> pdb=" O CYS C 115 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 49 " --> pdb=" O SER C 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 114 through 117 removed outlier: 3.543A pdb=" N TRP C 59 " --> pdb=" O CYS C 115 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 48 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN C 52 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE C 39 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N TRP C 54 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU C 37 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN C 56 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER C 35 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N SER C 58 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N SER C 33 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N THR C 60 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 10.051A pdb=" N TYR C 31 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 79 Processing sheet with id=AB4, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.581A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.581A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 117 Processing sheet with id=AB7, first strand: chain 'D' and resid 114 through 117 removed outlier: 3.959A pdb=" N VAL D 48 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 30 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 76 through 79 Processing sheet with id=AB9, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.586A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.586A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 114 through 117 Processing sheet with id=AC3, first strand: chain 'E' and resid 114 through 117 removed outlier: 3.920A pdb=" N VAL E 48 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 30 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 76 through 79 Processing sheet with id=AC5, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.563A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.563A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.605A pdb=" N LEU F 21 " --> pdb=" O LEU F 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.387A pdb=" N GLY F 11 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL F 119 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP F 37 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.387A pdb=" N GLY F 11 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL F 119 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR F 112 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.610A pdb=" N LEU G 21 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.388A pdb=" N GLY G 11 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 119 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP G 37 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.388A pdb=" N GLY G 11 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 119 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR G 112 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.623A pdb=" N LEU H 21 " --> pdb=" O LEU H 82 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.383A pdb=" N GLY H 11 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL H 119 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP H 37 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.383A pdb=" N GLY H 11 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL H 119 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR H 112 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 4 through 8 removed outlier: 3.612A pdb=" N LEU I 21 " --> pdb=" O LEU I 82 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.357A pdb=" N GLY I 11 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL I 119 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP I 37 " --> pdb=" O VAL I 49 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.357A pdb=" N GLY I 11 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL I 119 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR I 112 " --> pdb=" O ALA I 99 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 8 removed outlier: 3.622A pdb=" N LEU J 21 " --> pdb=" O LEU J 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.357A pdb=" N GLY J 11 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL J 119 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP J 37 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.357A pdb=" N GLY J 11 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL J 119 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR J 112 " --> pdb=" O ALA J 99 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1083 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: 4.56 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4245 1.34 - 1.46: 3300 1.46 - 1.57: 6310 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 13945 Sorted by residual: bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.20e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.98e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.92e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.83e+00 ... (remaining 13940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 17870 0.98 - 1.97: 829 1.97 - 2.95: 203 2.95 - 3.93: 52 3.93 - 4.91: 6 Bond angle restraints: 18960 Sorted by residual: angle pdb=" N GLY C 166 " pdb=" CA GLY C 166 " pdb=" C GLY C 166 " ideal model delta sigma weight residual 115.80 110.89 4.91 1.74e+00 3.30e-01 7.98e+00 angle pdb=" CA GLY C 166 " pdb=" C GLY C 166 " pdb=" N TYR C 167 " ideal model delta sigma weight residual 118.95 115.96 2.99 1.06e+00 8.90e-01 7.96e+00 angle pdb=" N GLY B 166 " pdb=" CA GLY B 166 " pdb=" C GLY B 166 " ideal model delta sigma weight residual 115.80 110.91 4.89 1.74e+00 3.30e-01 7.88e+00 angle pdb=" CA GLY B 166 " pdb=" C GLY B 166 " pdb=" N TYR B 167 " ideal model delta sigma weight residual 118.95 116.00 2.95 1.06e+00 8.90e-01 7.74e+00 angle pdb=" CA GLY B 166 " pdb=" C GLY B 166 " pdb=" O GLY B 166 " ideal model delta sigma weight residual 119.04 121.02 -1.98 9.10e-01 1.21e+00 4.72e+00 ... (remaining 18955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7315 17.94 - 35.88: 794 35.88 - 53.82: 193 53.82 - 71.76: 56 71.76 - 89.70: 12 Dihedral angle restraints: 8370 sinusoidal: 3605 harmonic: 4765 Sorted by residual: dihedral pdb=" CA LYS E 45 " pdb=" C LYS E 45 " pdb=" N ASN E 46 " pdb=" CA ASN E 46 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual -86.00 -112.75 26.75 1 1.00e+01 1.00e-02 1.03e+01 dihedral pdb=" CB CYS B 127 " pdb=" SG CYS B 127 " pdb=" SG CYS B 141 " pdb=" CB CYS B 141 " ideal model delta sinusoidal sigma weight residual -86.00 -112.41 26.41 1 1.00e+01 1.00e-02 1.00e+01 ... (remaining 8367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1437 0.040 - 0.079: 379 0.079 - 0.119: 183 0.119 - 0.158: 16 0.158 - 0.198: 5 Chirality restraints: 2020 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.25e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN E 110 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 110 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 2017 not shown) Planarity restraints: 2415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 79 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO B 80 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 79 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 80 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 79 " 0.038 5.00e-02 4.00e+02 5.88e-02 5.52e+00 pdb=" N PRO C 80 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.032 5.00e-02 4.00e+02 ... (remaining 2412 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 177 2.61 - 3.18: 11191 3.18 - 3.75: 17651 3.75 - 4.33: 26285 4.33 - 4.90: 45695 Nonbonded interactions: 100999 Sorted by model distance: nonbonded pdb=" N GLU F 90 " pdb=" OE1 GLU F 90 " model vdw 2.033 3.120 nonbonded pdb=" OG SER D 183 " pdb=" OD1 ASP D 196 " model vdw 2.046 3.040 nonbonded pdb=" OG SER B 183 " pdb=" OD1 ASP B 196 " model vdw 2.062 3.040 nonbonded pdb=" OG SER A 183 " pdb=" OD1 ASP A 196 " model vdw 2.063 3.040 nonbonded pdb=" OG SER C 183 " pdb=" OD1 ASP C 196 " model vdw 2.076 3.040 ... (remaining 100994 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 39.150 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 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 0.041 13945 Z= 0.189 Angle : 0.517 4.914 18960 Z= 0.267 Chirality : 0.043 0.198 2020 Planarity : 0.005 0.062 2400 Dihedral : 16.187 89.698 5325 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.14 % Allowed : 20.07 % Favored : 79.79 % 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: -3.17 (0.19), residues: 1620 helix: -3.56 (0.62), residues: 45 sheet: -1.10 (0.20), residues: 660 loop : -2.92 (0.17), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 133 HIS 0.002 0.001 HIS D 140 PHE 0.006 0.001 PHE I 69 TYR 0.011 0.001 TYR A 117 ARG 0.005 0.000 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 60 TYR cc_start: 0.8597 (m-80) cc_final: 0.8329 (m-10) REVERT: F 74 ASP cc_start: 0.7938 (t0) cc_final: 0.7689 (t0) REVERT: F 91 ASP cc_start: 0.9111 (m-30) cc_final: 0.8721 (m-30) REVERT: G 7 GLU cc_start: 0.8264 (mp0) cc_final: 0.7929 (mp0) REVERT: G 74 ASP cc_start: 0.7984 (t0) cc_final: 0.7737 (t0) REVERT: H 74 ASP cc_start: 0.8049 (t0) cc_final: 0.7731 (t0) REVERT: H 91 ASP cc_start: 0.9003 (m-30) cc_final: 0.8601 (m-30) REVERT: I 74 ASP cc_start: 0.7846 (t0) cc_final: 0.7617 (t0) REVERT: J 74 ASP cc_start: 0.8032 (t0) cc_final: 0.7749 (t0) outliers start: 2 outliers final: 1 residues processed: 298 average time/residue: 0.3453 time to fit residues: 137.3942 Evaluate side-chains 269 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 125 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13945 Z= 0.214 Angle : 0.695 8.959 18960 Z= 0.347 Chirality : 0.049 0.231 2020 Planarity : 0.006 0.058 2400 Dihedral : 10.532 71.923 2299 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 1.55 % Allowed : 18.17 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.19), residues: 1620 helix: -2.59 (0.70), residues: 45 sheet: -0.68 (0.20), residues: 665 loop : -2.94 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 133 HIS 0.003 0.001 HIS A 140 PHE 0.021 0.001 PHE D 134 TYR 0.025 0.001 TYR G 60 ARG 0.009 0.001 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 278 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 205 ARG cc_start: 0.8963 (ttm110) cc_final: 0.8665 (ttm110) REVERT: D 138 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8792 (t) REVERT: D 205 ARG cc_start: 0.8944 (ttm110) cc_final: 0.8624 (ttm110) REVERT: E 205 ARG cc_start: 0.8950 (ttm110) cc_final: 0.8676 (ttm110) REVERT: F 2 GLN cc_start: 0.8158 (mp10) cc_final: 0.7772 (pm20) REVERT: F 66 LYS cc_start: 0.9011 (tppt) cc_final: 0.8752 (tppp) REVERT: F 74 ASP cc_start: 0.8055 (t0) cc_final: 0.7840 (t0) REVERT: G 61 TYR cc_start: 0.8871 (m-80) cc_final: 0.8610 (m-80) REVERT: G 74 ASP cc_start: 0.8047 (t0) cc_final: 0.7804 (t0) REVERT: H 7 GLU cc_start: 0.8264 (mp0) cc_final: 0.8042 (mp0) REVERT: H 74 ASP cc_start: 0.8203 (t0) cc_final: 0.7885 (t0) REVERT: J 66 LYS cc_start: 0.8960 (tppt) cc_final: 0.8671 (tppt) REVERT: J 74 ASP cc_start: 0.8102 (t0) cc_final: 0.7796 (t0) outliers start: 22 outliers final: 11 residues processed: 289 average time/residue: 0.3386 time to fit residues: 131.6435 Evaluate side-chains 276 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 264 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 13945 Z= 0.442 Angle : 0.747 9.473 18960 Z= 0.372 Chirality : 0.049 0.239 2020 Planarity : 0.005 0.052 2400 Dihedral : 10.352 64.519 2295 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 1.97 % Allowed : 19.01 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.19), residues: 1620 helix: -1.90 (0.75), residues: 45 sheet: -0.79 (0.20), residues: 700 loop : -2.75 (0.18), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 133 HIS 0.002 0.001 HIS A 140 PHE 0.014 0.001 PHE I 69 TYR 0.019 0.002 TYR G 60 ARG 0.005 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 205 ARG cc_start: 0.8957 (ttm110) cc_final: 0.8629 (ttm110) REVERT: D 205 ARG cc_start: 0.8966 (ttm110) cc_final: 0.8620 (ttm110) REVERT: F 2 GLN cc_start: 0.8429 (mp10) cc_final: 0.8134 (mp10) REVERT: F 74 ASP cc_start: 0.8341 (t0) cc_final: 0.8105 (t0) REVERT: G 74 ASP cc_start: 0.8244 (t0) cc_final: 0.7967 (t0) REVERT: H 74 ASP cc_start: 0.8373 (t0) cc_final: 0.8083 (t0) REVERT: J 61 TYR cc_start: 0.8835 (m-80) cc_final: 0.8631 (m-80) REVERT: J 66 LYS cc_start: 0.9206 (tppt) cc_final: 0.8952 (tppt) REVERT: J 74 ASP cc_start: 0.8298 (t0) cc_final: 0.7987 (t0) outliers start: 28 outliers final: 20 residues processed: 280 average time/residue: 0.3398 time to fit residues: 127.8948 Evaluate side-chains 271 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 251 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13945 Z= 0.244 Angle : 0.687 9.476 18960 Z= 0.341 Chirality : 0.048 0.240 2020 Planarity : 0.005 0.052 2400 Dihedral : 9.490 59.797 2295 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.41 % Allowed : 20.07 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.20), residues: 1620 helix: -1.50 (0.80), residues: 45 sheet: -0.52 (0.21), residues: 645 loop : -2.57 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 133 HIS 0.003 0.001 HIS E 140 PHE 0.021 0.001 PHE A 134 TYR 0.014 0.001 TYR G 60 ARG 0.004 0.000 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 268 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8907 (ttm110) cc_final: 0.8616 (ttm110) REVERT: C 205 ARG cc_start: 0.8909 (ttm110) cc_final: 0.8603 (ttm110) REVERT: D 138 VAL cc_start: 0.9405 (OUTLIER) cc_final: 0.9165 (t) REVERT: D 205 ARG cc_start: 0.8937 (ttm110) cc_final: 0.8626 (ttm110) REVERT: F 2 GLN cc_start: 0.8435 (mp10) cc_final: 0.8058 (mp10) REVERT: F 74 ASP cc_start: 0.8279 (t0) cc_final: 0.8071 (t0) REVERT: G 74 ASP cc_start: 0.8266 (t0) cc_final: 0.8011 (t0) REVERT: G 84 MET cc_start: 0.8196 (mtm) cc_final: 0.7921 (ttm) REVERT: H 7 GLU cc_start: 0.8342 (mp0) cc_final: 0.8073 (mp0) REVERT: H 74 ASP cc_start: 0.8319 (t0) cc_final: 0.8027 (t0) REVERT: J 66 LYS cc_start: 0.9092 (tppt) cc_final: 0.8883 (tppt) REVERT: J 74 ASP cc_start: 0.8242 (t0) cc_final: 0.7935 (t0) outliers start: 20 outliers final: 14 residues processed: 284 average time/residue: 0.3379 time to fit residues: 128.7309 Evaluate side-chains 267 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 252 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13945 Z= 0.184 Angle : 0.675 9.536 18960 Z= 0.333 Chirality : 0.047 0.242 2020 Planarity : 0.004 0.053 2400 Dihedral : 8.611 59.116 2295 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.48 % Allowed : 20.35 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.19), residues: 1620 helix: -1.07 (0.79), residues: 45 sheet: -0.31 (0.20), residues: 670 loop : -2.59 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 133 HIS 0.003 0.001 HIS A 140 PHE 0.018 0.001 PHE B 134 TYR 0.011 0.001 TYR G 60 ARG 0.004 0.000 ARG G 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 268 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8901 (ttm110) cc_final: 0.8618 (ttm110) REVERT: C 138 VAL cc_start: 0.9400 (OUTLIER) cc_final: 0.9192 (t) REVERT: C 205 ARG cc_start: 0.8918 (ttm110) cc_final: 0.8658 (ttm110) REVERT: D 138 VAL cc_start: 0.9427 (OUTLIER) cc_final: 0.9201 (t) REVERT: F 2 GLN cc_start: 0.8430 (mp10) cc_final: 0.8005 (mp10) REVERT: F 66 LYS cc_start: 0.8988 (tppp) cc_final: 0.8691 (tppp) REVERT: F 69 PHE cc_start: 0.8227 (m-10) cc_final: 0.8019 (m-10) REVERT: F 74 ASP cc_start: 0.8282 (t0) cc_final: 0.8079 (t0) REVERT: G 74 ASP cc_start: 0.8272 (t0) cc_final: 0.7991 (t0) REVERT: H 74 ASP cc_start: 0.8316 (t0) cc_final: 0.8017 (t0) REVERT: J 74 ASP cc_start: 0.8267 (t0) cc_final: 0.7967 (t0) outliers start: 21 outliers final: 11 residues processed: 286 average time/residue: 0.3364 time to fit residues: 130.0385 Evaluate side-chains 273 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 260 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 154 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13945 Z= 0.200 Angle : 0.673 9.550 18960 Z= 0.331 Chirality : 0.047 0.242 2020 Planarity : 0.004 0.051 2400 Dihedral : 8.084 59.551 2295 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.41 % Allowed : 20.63 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.20), residues: 1620 helix: -0.57 (0.79), residues: 45 sheet: -0.21 (0.21), residues: 625 loop : -2.40 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 133 HIS 0.003 0.001 HIS E 140 PHE 0.023 0.001 PHE D 134 TYR 0.012 0.001 TYR I 60 ARG 0.005 0.000 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8904 (ttm110) cc_final: 0.8674 (ttm110) REVERT: C 138 VAL cc_start: 0.9400 (OUTLIER) cc_final: 0.9192 (t) REVERT: C 205 ARG cc_start: 0.8937 (ttm110) cc_final: 0.8705 (ttm110) REVERT: D 138 VAL cc_start: 0.9450 (OUTLIER) cc_final: 0.9224 (t) REVERT: E 138 VAL cc_start: 0.9378 (OUTLIER) cc_final: 0.9133 (t) REVERT: F 7 GLU cc_start: 0.8267 (mp0) cc_final: 0.7932 (mp0) REVERT: F 66 LYS cc_start: 0.8973 (tppp) cc_final: 0.8643 (tppp) REVERT: G 74 ASP cc_start: 0.8293 (t0) cc_final: 0.8040 (t0) REVERT: H 74 ASP cc_start: 0.8353 (t0) cc_final: 0.8114 (t0) REVERT: J 74 ASP cc_start: 0.8296 (t0) cc_final: 0.8041 (t0) outliers start: 20 outliers final: 12 residues processed: 277 average time/residue: 0.3349 time to fit residues: 125.5218 Evaluate side-chains 271 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 256 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 87 optimal weight: 0.0670 chunk 130 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13945 Z= 0.346 Angle : 0.720 10.344 18960 Z= 0.354 Chirality : 0.048 0.243 2020 Planarity : 0.004 0.049 2400 Dihedral : 8.229 59.998 2295 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 1.34 % Allowed : 21.41 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.20), residues: 1620 helix: -0.23 (0.77), residues: 45 sheet: -0.20 (0.21), residues: 625 loop : -2.40 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 133 HIS 0.003 0.001 HIS E 140 PHE 0.021 0.001 PHE I 69 TYR 0.014 0.001 TYR C 71 ARG 0.005 0.000 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 259 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8925 (ttm110) cc_final: 0.8642 (ttm110) REVERT: B 181 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8594 (ttmm) REVERT: C 138 VAL cc_start: 0.9432 (OUTLIER) cc_final: 0.9230 (t) REVERT: C 205 ARG cc_start: 0.8929 (ttm110) cc_final: 0.8657 (ttm110) REVERT: D 138 VAL cc_start: 0.9481 (OUTLIER) cc_final: 0.9269 (t) REVERT: E 138 VAL cc_start: 0.9419 (OUTLIER) cc_final: 0.9174 (t) REVERT: F 7 GLU cc_start: 0.8248 (mp0) cc_final: 0.7979 (mp0) REVERT: F 69 PHE cc_start: 0.8119 (m-10) cc_final: 0.7913 (m-10) REVERT: G 74 ASP cc_start: 0.8378 (t0) cc_final: 0.8110 (t0) REVERT: H 74 ASP cc_start: 0.8402 (t0) cc_final: 0.8145 (t0) REVERT: J 66 LYS cc_start: 0.9014 (ttmm) cc_final: 0.8754 (ttmt) REVERT: J 74 ASP cc_start: 0.8366 (t0) cc_final: 0.8141 (t0) outliers start: 19 outliers final: 11 residues processed: 272 average time/residue: 0.3367 time to fit residues: 123.3090 Evaluate side-chains 263 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 248 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13945 Z= 0.189 Angle : 0.686 10.097 18960 Z= 0.336 Chirality : 0.047 0.238 2020 Planarity : 0.004 0.048 2400 Dihedral : 7.770 59.475 2295 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.13 % Allowed : 21.34 % Favored : 77.54 % 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: -1.87 (0.20), residues: 1620 helix: 0.39 (0.80), residues: 45 sheet: 0.02 (0.20), residues: 670 loop : -2.46 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 133 HIS 0.004 0.001 HIS E 140 PHE 0.028 0.001 PHE A 134 TYR 0.009 0.001 TYR I 112 ARG 0.005 0.000 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 246 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8875 (ttm110) cc_final: 0.8605 (ttm110) REVERT: C 205 ARG cc_start: 0.8907 (ttm110) cc_final: 0.8672 (ttm-80) REVERT: D 138 VAL cc_start: 0.9468 (OUTLIER) cc_final: 0.9254 (t) REVERT: E 138 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9170 (t) REVERT: F 66 LYS cc_start: 0.9042 (tppp) cc_final: 0.8774 (tppp) REVERT: G 74 ASP cc_start: 0.8359 (t0) cc_final: 0.8096 (t0) REVERT: H 74 ASP cc_start: 0.8354 (t0) cc_final: 0.8093 (t0) REVERT: J 12 LEU cc_start: 0.9090 (tp) cc_final: 0.8884 (tp) REVERT: J 66 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8615 (ttmt) REVERT: J 74 ASP cc_start: 0.8320 (t0) cc_final: 0.8084 (t0) outliers start: 16 outliers final: 10 residues processed: 260 average time/residue: 0.3411 time to fit residues: 119.2223 Evaluate side-chains 252 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13945 Z= 0.191 Angle : 0.700 11.215 18960 Z= 0.342 Chirality : 0.047 0.242 2020 Planarity : 0.004 0.049 2400 Dihedral : 7.563 58.187 2295 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 1.06 % Allowed : 21.55 % Favored : 77.39 % 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: -1.72 (0.20), residues: 1620 helix: 1.04 (0.80), residues: 45 sheet: 0.15 (0.20), residues: 670 loop : -2.42 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 133 HIS 0.004 0.001 HIS C 140 PHE 0.026 0.001 PHE E 134 TYR 0.009 0.001 TYR D 117 ARG 0.006 0.000 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 242 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8845 (ttm110) cc_final: 0.8587 (ttm110) REVERT: B 133 TRP cc_start: 0.8156 (m-90) cc_final: 0.7855 (m-90) REVERT: C 205 ARG cc_start: 0.8871 (ttm110) cc_final: 0.8638 (ttm-80) REVERT: D 138 VAL cc_start: 0.9456 (OUTLIER) cc_final: 0.9243 (t) REVERT: E 138 VAL cc_start: 0.9390 (OUTLIER) cc_final: 0.9174 (t) REVERT: F 66 LYS cc_start: 0.9019 (tppp) cc_final: 0.8775 (tppp) REVERT: G 74 ASP cc_start: 0.8386 (t0) cc_final: 0.8137 (t0) REVERT: H 74 ASP cc_start: 0.8373 (t0) cc_final: 0.8114 (t0) REVERT: I 77 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9150 (ptpp) REVERT: J 66 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8524 (ttmt) REVERT: J 74 ASP cc_start: 0.8329 (t0) cc_final: 0.8103 (t0) outliers start: 15 outliers final: 11 residues processed: 253 average time/residue: 0.3437 time to fit residues: 116.9450 Evaluate side-chains 250 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 146 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13945 Z= 0.198 Angle : 0.698 11.888 18960 Z= 0.339 Chirality : 0.047 0.242 2020 Planarity : 0.004 0.050 2400 Dihedral : 7.446 58.017 2295 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.99 % Allowed : 21.55 % Favored : 77.46 % 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: -1.63 (0.20), residues: 1620 helix: 1.41 (0.81), residues: 45 sheet: 0.31 (0.20), residues: 670 loop : -2.47 (0.17), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 133 HIS 0.003 0.001 HIS E 140 PHE 0.037 0.001 PHE I 69 TYR 0.010 0.001 TYR I 81 ARG 0.006 0.000 ARG H 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 244 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8842 (ttm110) cc_final: 0.8588 (ttm110) REVERT: B 133 TRP cc_start: 0.8190 (m-90) cc_final: 0.7939 (m-90) REVERT: C 205 ARG cc_start: 0.8875 (ttm110) cc_final: 0.8628 (ttm110) REVERT: D 138 VAL cc_start: 0.9460 (OUTLIER) cc_final: 0.9247 (t) REVERT: E 138 VAL cc_start: 0.9382 (OUTLIER) cc_final: 0.9171 (t) REVERT: F 66 LYS cc_start: 0.9022 (tppp) cc_final: 0.8786 (tppp) REVERT: G 74 ASP cc_start: 0.8389 (t0) cc_final: 0.8152 (t0) REVERT: H 74 ASP cc_start: 0.8429 (t0) cc_final: 0.8183 (t0) REVERT: I 77 LYS cc_start: 0.9410 (ptpp) cc_final: 0.9133 (ptpp) REVERT: J 74 ASP cc_start: 0.8360 (t0) cc_final: 0.8143 (t0) outliers start: 14 outliers final: 12 residues processed: 254 average time/residue: 0.3930 time to fit residues: 134.1640 Evaluate side-chains 251 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 237 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.062140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.043794 restraints weight = 74619.140| |-----------------------------------------------------------------------------| r_work (start): 0.2496 rms_B_bonded: 5.10 r_work: 0.2311 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2323 r_free = 0.2323 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2323 r_free = 0.2323 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13945 Z= 0.311 Angle : 0.725 12.399 18960 Z= 0.354 Chirality : 0.047 0.244 2020 Planarity : 0.004 0.049 2400 Dihedral : 7.718 59.701 2295 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.06 % Allowed : 21.97 % Favored : 76.97 % 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: -1.78 (0.19), residues: 1620 helix: 1.26 (0.79), residues: 45 sheet: 0.15 (0.20), residues: 655 loop : -2.47 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 133 HIS 0.003 0.001 HIS E 140 PHE 0.039 0.001 PHE I 69 TYR 0.012 0.001 TYR C 71 ARG 0.007 0.001 ARG H 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3351.24 seconds wall clock time: 61 minutes 50.96 seconds (3710.96 seconds total)