Starting phenix.real_space_refine on Fri Nov 15 03:14:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c2b_45153/11_2024/9c2b_45153.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c2b_45153/11_2024/9c2b_45153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c2b_45153/11_2024/9c2b_45153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c2b_45153/11_2024/9c2b_45153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c2b_45153/11_2024/9c2b_45153.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c2b_45153/11_2024/9c2b_45153.cif" } resolution = 2.42 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= 0.001 sd= 0.030 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 42 5.16 5 C 5178 2.51 5 N 1350 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8208 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2576 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2576 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2576 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Time building chain proxies: 6.72, per 1000 atoms: 0.82 Number of scatterers: 8208 At special positions: 0 Unit cell: (90.832, 88.8856, 118.082, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 9 15.00 Mg 3 11.99 O 1626 8.00 N 1350 7.00 C 5178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 149 " distance=2.04 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 270 " 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 502 " - " ASN A 242 " " NAG B 502 " - " ASN B 242 " " NAG C 403 " - " ASN C 242 " " NAG D 1 " - " ASN A 153 " " NAG E 1 " - " ASN A 184 " " NAG F 1 " - " ASN B 153 " " NAG G 1 " - " ASN B 184 " " NAG H 1 " - " ASN C 153 " " NAG I 1 " - " ASN C 184 " Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 946.8 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 30.7% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 210 through 217 removed outlier: 3.565A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.691A pdb=" N GLU A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 327 through 356 Processing helix chain 'B' and resid 28 through 47 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 210 through 217 removed outlier: 3.564A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.691A pdb=" N GLU B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 327 through 356 Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 210 through 217 removed outlier: 3.565A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.690A pdb=" N GLU C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 327 through 356 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 60 current: chain 'A' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 99 through 118 current: chain 'A' and resid 157 through 165 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 157 through 165 current: chain 'A' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 273 through 277 current: chain 'A' and resid 302 through 326 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 60 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 60 current: chain 'B' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 99 through 118 current: chain 'B' and resid 157 through 165 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 157 through 165 current: chain 'B' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 273 through 277 current: chain 'B' and resid 302 through 326 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 70 Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 76 Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 60 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 60 current: chain 'C' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 99 through 118 current: chain 'C' and resid 157 through 165 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 157 through 165 current: chain 'C' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 277 current: chain 'C' and resid 302 through 326 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 62 through 70 Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 76 241 hydrogen bonds defined for protein. 606 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: 2.14 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2523 1.34 - 1.46: 1934 1.46 - 1.58: 3754 1.58 - 1.70: 12 1.70 - 1.82: 51 Bond restraints: 8274 Sorted by residual: bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.435 -0.047 1.00e-02 1.00e+04 2.17e+01 bond pdb=" C4 ATP A 500 " pdb=" C5 ATP A 500 " ideal model delta sigma weight residual 1.388 1.434 -0.046 1.00e-02 1.00e+04 2.13e+01 bond pdb=" C4 ATP B 500 " pdb=" C5 ATP B 500 " ideal model delta sigma weight residual 1.388 1.434 -0.046 1.00e-02 1.00e+04 2.09e+01 bond pdb=" C4 ATP A 500 " pdb=" N9 ATP A 500 " ideal model delta sigma weight residual 1.374 1.334 0.040 1.00e-02 1.00e+04 1.57e+01 bond pdb=" C8 ATP B 500 " pdb=" N7 ATP B 500 " ideal model delta sigma weight residual 1.310 1.349 -0.039 1.00e-02 1.00e+04 1.54e+01 ... (remaining 8269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 11195 3.69 - 7.39: 52 7.39 - 11.08: 3 11.08 - 14.78: 0 14.78 - 18.47: 6 Bond angle restraints: 11256 Sorted by residual: angle pdb=" PB ATP A 500 " pdb=" O3B ATP A 500 " pdb=" PG ATP A 500 " ideal model delta sigma weight residual 139.87 121.40 18.47 1.00e+00 1.00e+00 3.41e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 121.41 18.46 1.00e+00 1.00e+00 3.41e+02 angle pdb=" PB ATP B 500 " pdb=" O3B ATP B 500 " pdb=" PG ATP B 500 " ideal model delta sigma weight residual 139.87 121.44 18.43 1.00e+00 1.00e+00 3.40e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 121.74 15.09 1.00e+00 1.00e+00 2.28e+02 angle pdb=" PA ATP A 500 " pdb=" O3A ATP A 500 " pdb=" PB ATP A 500 " ideal model delta sigma weight residual 136.83 121.79 15.04 1.00e+00 1.00e+00 2.26e+02 ... (remaining 11251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 4551 21.12 - 42.24: 419 42.24 - 63.35: 94 63.35 - 84.47: 21 84.47 - 105.59: 21 Dihedral angle restraints: 5106 sinusoidal: 2298 harmonic: 2808 Sorted by residual: dihedral pdb=" CA PHE B 308 " pdb=" C PHE B 308 " pdb=" N LYS B 309 " pdb=" CA LYS B 309 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA PHE C 308 " pdb=" C PHE C 308 " pdb=" N LYS C 309 " pdb=" CA LYS C 309 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA PHE A 308 " pdb=" C PHE A 308 " pdb=" N LYS A 309 " pdb=" CA LYS A 309 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 5103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 866 0.052 - 0.103: 289 0.103 - 0.155: 120 0.155 - 0.206: 18 0.206 - 0.258: 9 Chirality restraints: 1302 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.82e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.72e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.68e+01 ... (remaining 1299 not shown) Planarity restraints: 1404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.085 2.00e-02 2.50e+03 7.04e-02 6.20e+01 pdb=" C7 NAG D 1 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.111 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.085 2.00e-02 2.50e+03 7.01e-02 6.14e+01 pdb=" C7 NAG F 1 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.111 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.085 2.00e-02 2.50e+03 7.00e-02 6.13e+01 pdb=" C7 NAG H 1 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.111 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.012 2.00e-02 2.50e+03 ... (remaining 1401 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 393 2.71 - 3.26: 7929 3.26 - 3.80: 14664 3.80 - 4.35: 18955 4.35 - 4.90: 29682 Nonbonded interactions: 71623 Sorted by model distance: nonbonded pdb=" O1G ATP B 500 " pdb="MG MG C 402 " model vdw 2.161 2.170 nonbonded pdb=" O1G ATP A 500 " pdb="MG MG B 501 " model vdw 2.161 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1G ATP C 401 " model vdw 2.162 2.170 nonbonded pdb=" O HOH A 608 " pdb=" O HOH A 645 " model vdw 2.218 3.040 nonbonded pdb=" O HOH B 608 " pdb=" O HOH B 645 " model vdw 2.226 3.040 ... (remaining 71618 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 27 through 356) selection = (chain 'B' and resid 27 through 356) selection = (chain 'C' and resid 27 through 356) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' 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 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: 6.060 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.150 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 8274 Z= 0.451 Angle : 0.976 18.470 11256 Z= 0.707 Chirality : 0.063 0.258 1302 Planarity : 0.007 0.070 1395 Dihedral : 18.261 105.589 3276 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.27 (0.27), residues: 984 helix: -0.27 (0.33), residues: 273 sheet: 0.47 (0.28), residues: 309 loop : 0.52 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 85 HIS 0.004 0.001 HIS A 355 PHE 0.013 0.002 PHE A 276 TYR 0.019 0.002 TYR B 51 ARG 0.007 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: C 215 LYS cc_start: 0.8178 (tttp) cc_final: 0.7892 (ttmm) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 1.5338 time to fit residues: 206.4963 Evaluate side-chains 115 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.2980 chunk 75 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 0.0370 chunk 89 optimal weight: 0.5980 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8274 Z= 0.209 Angle : 0.572 7.348 11256 Z= 0.297 Chirality : 0.046 0.180 1302 Planarity : 0.004 0.045 1395 Dihedral : 12.877 89.640 1530 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.66 % Allowed : 16.79 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.05 (0.28), residues: 984 helix: 1.21 (0.34), residues: 273 sheet: 0.51 (0.28), residues: 309 loop : 0.69 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 85 HIS 0.003 0.001 HIS B 220 PHE 0.014 0.002 PHE A 326 TYR 0.017 0.002 TYR C 90 ARG 0.007 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.027 Fit side-chains REVERT: A 275 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: B 138 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7781 (tttt) REVERT: B 197 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7644 (ttm110) REVERT: B 215 LYS cc_start: 0.8116 (tttp) cc_final: 0.7839 (ttmm) REVERT: B 275 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: C 52 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7299 (mt-10) REVERT: C 138 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7762 (tttt) REVERT: C 148 LYS cc_start: 0.8290 (mppt) cc_final: 0.7809 (mmtt) outliers start: 22 outliers final: 5 residues processed: 134 average time/residue: 1.4253 time to fit residues: 201.9871 Evaluate side-chains 126 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 138 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN C 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8274 Z= 0.196 Angle : 0.547 6.519 11256 Z= 0.282 Chirality : 0.045 0.183 1302 Planarity : 0.004 0.044 1395 Dihedral : 11.258 89.611 1530 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.78 % Allowed : 18.12 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.17 (0.28), residues: 984 helix: 1.48 (0.34), residues: 273 sheet: 0.45 (0.27), residues: 309 loop : 0.76 (0.35), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 259 HIS 0.002 0.001 HIS C 260 PHE 0.010 0.002 PHE B 243 TYR 0.016 0.001 TYR C 90 ARG 0.007 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.921 Fit side-chains REVERT: A 138 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7957 (tttt) REVERT: A 275 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: A 332 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.5368 (mpm) REVERT: B 138 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7780 (tttt) REVERT: B 197 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7642 (ttm110) REVERT: B 215 LYS cc_start: 0.8114 (tttp) cc_final: 0.7839 (ttmm) REVERT: B 275 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: B 332 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.5535 (mpm) REVERT: C 138 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7820 (tttt) REVERT: C 148 LYS cc_start: 0.8264 (mppt) cc_final: 0.7804 (mmtt) REVERT: C 215 LYS cc_start: 0.8127 (tttp) cc_final: 0.7867 (ttmm) REVERT: C 332 MET cc_start: 0.7629 (mpp) cc_final: 0.7383 (mpm) outliers start: 23 outliers final: 7 residues processed: 134 average time/residue: 1.4196 time to fit residues: 201.0384 Evaluate side-chains 129 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 138 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 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 114 GLN A 237 GLN B 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8274 Z= 0.203 Angle : 0.544 7.028 11256 Z= 0.280 Chirality : 0.046 0.197 1302 Planarity : 0.004 0.044 1395 Dihedral : 10.216 88.507 1530 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.38 % Allowed : 17.39 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.26 (0.28), residues: 984 helix: 1.60 (0.35), residues: 273 sheet: 0.52 (0.27), residues: 324 loop : 0.76 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 259 HIS 0.002 0.001 HIS C 260 PHE 0.011 0.002 PHE A 243 TYR 0.016 0.001 TYR C 90 ARG 0.007 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.988 Fit side-chains REVERT: A 138 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7945 (tttt) REVERT: A 275 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: A 332 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.5330 (mpm) REVERT: B 138 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7776 (tttt) REVERT: B 197 ARG cc_start: 0.8011 (ttm-80) cc_final: 0.7647 (ttm110) REVERT: B 215 LYS cc_start: 0.8111 (tttp) cc_final: 0.7846 (ttmm) REVERT: B 267 VAL cc_start: 0.7882 (m) cc_final: 0.7528 (p) REVERT: B 275 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: B 332 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.5547 (mpm) REVERT: C 52 GLU cc_start: 0.7683 (tp30) cc_final: 0.7315 (mt-10) REVERT: C 138 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7847 (tttt) REVERT: C 148 LYS cc_start: 0.8266 (mppt) cc_final: 0.7785 (mmtt) outliers start: 28 outliers final: 12 residues processed: 139 average time/residue: 1.4196 time to fit residues: 208.5351 Evaluate side-chains 135 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.0170 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.0030 chunk 81 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.4228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8274 Z= 0.151 Angle : 0.509 7.222 11256 Z= 0.262 Chirality : 0.044 0.139 1302 Planarity : 0.004 0.043 1395 Dihedral : 9.479 88.446 1530 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.02 % Allowed : 17.75 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.30 (0.29), residues: 984 helix: 1.67 (0.35), residues: 273 sheet: 0.66 (0.29), residues: 297 loop : 0.65 (0.34), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 259 HIS 0.001 0.001 HIS B 355 PHE 0.008 0.001 PHE B 230 TYR 0.015 0.001 TYR C 90 ARG 0.007 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.854 Fit side-chains REVERT: A 52 GLU cc_start: 0.7677 (tp30) cc_final: 0.7388 (mt-10) REVERT: A 138 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7950 (tttt) REVERT: A 275 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: A 332 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.5357 (mpm) REVERT: B 138 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7754 (tttt) REVERT: B 215 LYS cc_start: 0.8073 (tttp) cc_final: 0.7810 (ttmm) REVERT: B 267 VAL cc_start: 0.7844 (m) cc_final: 0.7559 (p) REVERT: B 275 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: B 332 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.5567 (mpm) REVERT: C 52 GLU cc_start: 0.7670 (tp30) cc_final: 0.7320 (mt-10) REVERT: C 148 LYS cc_start: 0.8269 (mppt) cc_final: 0.7808 (mmtt) REVERT: C 332 MET cc_start: 0.7655 (mpp) cc_final: 0.7437 (mpm) outliers start: 25 outliers final: 9 residues processed: 138 average time/residue: 1.4287 time to fit residues: 208.1906 Evaluate side-chains 135 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 0.2980 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8274 Z= 0.242 Angle : 0.556 7.588 11256 Z= 0.288 Chirality : 0.045 0.165 1302 Planarity : 0.004 0.043 1395 Dihedral : 9.529 89.889 1530 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.38 % Allowed : 17.87 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.29 (0.28), residues: 984 helix: 1.68 (0.35), residues: 273 sheet: 0.52 (0.27), residues: 324 loop : 0.76 (0.36), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 259 HIS 0.002 0.001 HIS C 260 PHE 0.011 0.002 PHE A 276 TYR 0.015 0.002 TYR C 90 ARG 0.008 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7977 (tttt) REVERT: A 275 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: A 332 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.5432 (mpm) REVERT: B 138 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7807 (tttt) REVERT: B 215 LYS cc_start: 0.8116 (tttp) cc_final: 0.7856 (ttmm) REVERT: B 267 VAL cc_start: 0.7871 (m) cc_final: 0.7566 (p) REVERT: B 275 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: B 332 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.5617 (mpm) REVERT: C 52 GLU cc_start: 0.7713 (tp30) cc_final: 0.7340 (mt-10) REVERT: C 138 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7876 (tttt) REVERT: C 148 LYS cc_start: 0.8270 (mppt) cc_final: 0.7779 (mmtt) REVERT: C 246 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8426 (mp) REVERT: C 332 MET cc_start: 0.7617 (tpp) cc_final: 0.7394 (mpm) outliers start: 28 outliers final: 12 residues processed: 132 average time/residue: 1.4186 time to fit residues: 197.5863 Evaluate side-chains 133 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 275 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 0.0010 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8274 Z= 0.209 Angle : 0.537 7.876 11256 Z= 0.279 Chirality : 0.045 0.145 1302 Planarity : 0.004 0.043 1395 Dihedral : 9.350 89.539 1530 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.14 % Allowed : 18.24 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.31 (0.28), residues: 984 helix: 1.73 (0.35), residues: 273 sheet: 0.52 (0.27), residues: 324 loop : 0.75 (0.36), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 259 HIS 0.002 0.001 HIS C 260 PHE 0.010 0.002 PHE B 276 TYR 0.016 0.001 TYR C 90 ARG 0.008 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.907 Fit side-chains REVERT: A 52 GLU cc_start: 0.7684 (tp30) cc_final: 0.7370 (mt-10) REVERT: A 138 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7973 (tttt) REVERT: A 275 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: A 332 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.5443 (mpm) REVERT: B 138 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7803 (tttt) REVERT: B 215 LYS cc_start: 0.8119 (tttp) cc_final: 0.7860 (ttmm) REVERT: B 267 VAL cc_start: 0.7871 (m) cc_final: 0.7581 (p) REVERT: B 275 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: B 332 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.5613 (mpm) REVERT: C 52 GLU cc_start: 0.7711 (tp30) cc_final: 0.7343 (mt-10) REVERT: C 138 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7856 (tttt) REVERT: C 148 LYS cc_start: 0.8262 (mppt) cc_final: 0.7772 (mmtt) outliers start: 26 outliers final: 12 residues processed: 135 average time/residue: 1.4994 time to fit residues: 213.7141 Evaluate side-chains 138 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.0670 chunk 83 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8274 Z= 0.166 Angle : 0.534 8.202 11256 Z= 0.282 Chirality : 0.045 0.295 1302 Planarity : 0.004 0.042 1395 Dihedral : 9.260 87.736 1530 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.78 % Allowed : 18.84 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.34 (0.29), residues: 984 helix: 1.79 (0.35), residues: 273 sheet: 0.52 (0.27), residues: 324 loop : 0.77 (0.36), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 259 HIS 0.002 0.000 HIS A 296 PHE 0.010 0.001 PHE B 243 TYR 0.014 0.001 TYR B 90 ARG 0.009 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.954 Fit side-chains REVERT: A 52 GLU cc_start: 0.7688 (tp30) cc_final: 0.7374 (mt-10) REVERT: A 138 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7945 (tttt) REVERT: A 267 VAL cc_start: 0.7911 (m) cc_final: 0.7634 (p) REVERT: A 275 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: A 332 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.5430 (mpm) REVERT: B 215 LYS cc_start: 0.8095 (tttp) cc_final: 0.7835 (ttmm) REVERT: B 242 ASN cc_start: 0.6639 (OUTLIER) cc_final: 0.5801 (t0) REVERT: B 267 VAL cc_start: 0.7842 (m) cc_final: 0.7588 (p) REVERT: B 332 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.5582 (mpm) REVERT: C 52 GLU cc_start: 0.7692 (tp30) cc_final: 0.7342 (mt-10) REVERT: C 148 LYS cc_start: 0.8242 (mppt) cc_final: 0.7787 (mmtt) REVERT: C 215 LYS cc_start: 0.8124 (tttp) cc_final: 0.7851 (ttmm) REVERT: C 267 VAL cc_start: 0.7805 (m) cc_final: 0.7516 (p) outliers start: 23 outliers final: 10 residues processed: 136 average time/residue: 1.3945 time to fit residues: 200.3824 Evaluate side-chains 134 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 84 optimal weight: 0.0980 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 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 114 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8274 Z= 0.185 Angle : 0.555 8.284 11256 Z= 0.292 Chirality : 0.045 0.213 1302 Planarity : 0.004 0.043 1395 Dihedral : 9.472 87.477 1530 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.66 % Allowed : 18.96 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.36 (0.29), residues: 984 helix: 1.80 (0.35), residues: 273 sheet: 0.53 (0.27), residues: 324 loop : 0.77 (0.36), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 259 HIS 0.001 0.001 HIS B 277 PHE 0.013 0.001 PHE A 243 TYR 0.014 0.001 TYR C 90 ARG 0.008 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.928 Fit side-chains REVERT: A 52 GLU cc_start: 0.7688 (tp30) cc_final: 0.7392 (mt-10) REVERT: A 138 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7948 (tttt) REVERT: A 267 VAL cc_start: 0.7900 (m) cc_final: 0.7623 (p) REVERT: A 275 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: A 332 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.5436 (mpm) REVERT: B 138 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7794 (tttt) REVERT: B 215 LYS cc_start: 0.8109 (tttp) cc_final: 0.7848 (ttmm) REVERT: B 242 ASN cc_start: 0.6174 (OUTLIER) cc_final: 0.5696 (m-40) REVERT: B 267 VAL cc_start: 0.7848 (m) cc_final: 0.7595 (p) REVERT: B 332 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.5590 (mpm) REVERT: C 52 GLU cc_start: 0.7712 (tp30) cc_final: 0.7355 (mt-10) REVERT: C 148 LYS cc_start: 0.8243 (mppt) cc_final: 0.7768 (mmtt) REVERT: C 215 LYS cc_start: 0.8133 (tttp) cc_final: 0.7860 (ttmm) REVERT: C 267 VAL cc_start: 0.7794 (m) cc_final: 0.7512 (p) REVERT: C 332 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.5432 (mpm) outliers start: 22 outliers final: 10 residues processed: 130 average time/residue: 1.4714 time to fit residues: 201.4663 Evaluate side-chains 135 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 0.0050 chunk 62 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8274 Z= 0.191 Angle : 0.558 8.324 11256 Z= 0.291 Chirality : 0.045 0.214 1302 Planarity : 0.004 0.043 1395 Dihedral : 9.343 87.598 1530 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.42 % Allowed : 19.32 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.37 (0.29), residues: 984 helix: 1.81 (0.36), residues: 273 sheet: 0.53 (0.27), residues: 324 loop : 0.79 (0.36), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 259 HIS 0.002 0.001 HIS B 277 PHE 0.009 0.001 PHE A 276 TYR 0.014 0.001 TYR C 90 ARG 0.008 0.000 ARG B 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.833 Fit side-chains REVERT: A 52 GLU cc_start: 0.7696 (tp30) cc_final: 0.7391 (mt-10) REVERT: A 138 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7948 (tttt) REVERT: A 267 VAL cc_start: 0.7904 (m) cc_final: 0.7641 (p) REVERT: A 275 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: A 332 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.5458 (mpm) REVERT: B 138 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7794 (tttt) REVERT: B 215 LYS cc_start: 0.8112 (tttp) cc_final: 0.7853 (ttmm) REVERT: B 242 ASN cc_start: 0.5866 (OUTLIER) cc_final: 0.5519 (m-40) REVERT: B 267 VAL cc_start: 0.7844 (m) cc_final: 0.7600 (p) REVERT: B 332 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.5591 (mpm) REVERT: C 52 GLU cc_start: 0.7719 (tp30) cc_final: 0.7359 (mt-10) REVERT: C 138 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7850 (tttt) REVERT: C 148 LYS cc_start: 0.8245 (mppt) cc_final: 0.7768 (mmtt) REVERT: C 215 LYS cc_start: 0.8136 (tttp) cc_final: 0.7863 (ttmm) REVERT: C 267 VAL cc_start: 0.7790 (m) cc_final: 0.7513 (p) outliers start: 20 outliers final: 11 residues processed: 127 average time/residue: 1.5292 time to fit residues: 204.4704 Evaluate side-chains 136 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.164427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117218 restraints weight = 7335.371| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.66 r_work: 0.3280 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8274 Z= 0.172 Angle : 0.536 8.323 11256 Z= 0.278 Chirality : 0.045 0.171 1302 Planarity : 0.004 0.042 1395 Dihedral : 9.036 85.492 1530 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.54 % Allowed : 19.08 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.41 (0.29), residues: 984 helix: 1.84 (0.36), residues: 273 sheet: 0.57 (0.27), residues: 324 loop : 0.80 (0.36), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 259 HIS 0.002 0.001 HIS B 277 PHE 0.008 0.001 PHE C 276 TYR 0.014 0.001 TYR B 90 ARG 0.008 0.000 ARG B 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3962.71 seconds wall clock time: 71 minutes 35.65 seconds (4295.65 seconds total)