Starting phenix.real_space_refine on Sun May 11 15:05:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c2b_45153/05_2025/9c2b_45153.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c2b_45153/05_2025/9c2b_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/cci-nas-00/data/ceres_data/9c2b_45153/05_2025/9c2b_45153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c2b_45153/05_2025/9c2b_45153.map" model { file = "/net/cci-nas-00/data/ceres_data/9c2b_45153/05_2025/9c2b_45153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c2b_45153/05_2025/9c2b_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-5687/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: 6.54, per 1000 atoms: 0.80 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: 2.53 Conformation dependent library (CDL) restraints added in 969.3 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: 0.83 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: 2.02 Time building geometry restraints manager: 2.86 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: 0.03 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: 5.850 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: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.090 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.300 ------------------------------------------------------------------------------- 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 8304 Z= 0.446 Angle : 0.991 18.470 11334 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00904 ( 9) link_NAG-ASN : angle 3.45262 ( 27) link_BETA1-4 : bond 0.00290 ( 9) link_BETA1-4 : angle 1.38228 ( 27) hydrogen bonds : bond 0.16394 ( 241) hydrogen bonds : angle 6.24701 ( 606) SS BOND : bond 0.00273 ( 12) SS BOND : angle 1.10238 ( 24) covalent geometry : bond 0.00697 ( 8274) covalent geometry : angle 0.97577 (11256) *********************** 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 : 0.877 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: 1.5230 time to fit residues: 204.7045 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 : 0.854 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.7980 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: 0.7460 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114843 restraints weight = 7337.542| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.67 r_work: 0.3242 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8304 Z= 0.146 Angle : 0.592 7.450 11334 Z= 0.300 Chirality : 0.046 0.172 1302 Planarity : 0.004 0.045 1395 Dihedral : 12.727 89.330 1530 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.54 % Allowed : 17.15 % Favored : 80.31 % 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: 0.52 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 9) link_NAG-ASN : angle 2.37668 ( 27) link_BETA1-4 : bond 0.00596 ( 9) link_BETA1-4 : angle 1.97882 ( 27) hydrogen bonds : bond 0.03662 ( 241) hydrogen bonds : angle 4.72284 ( 606) SS BOND : bond 0.00304 ( 12) SS BOND : angle 1.12994 ( 24) covalent geometry : bond 0.00325 ( 8274) covalent geometry : angle 0.57237 (11256) *********************** 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 138 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.877 Fit side-chains REVERT: A 52 GLU cc_start: 0.7949 (tp30) cc_final: 0.7632 (mt-10) REVERT: A 275 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: B 138 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8199 (tttt) REVERT: B 197 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.7894 (ttm110) REVERT: B 215 LYS cc_start: 0.8375 (tttp) cc_final: 0.7990 (ttmm) REVERT: B 275 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: C 52 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7557 (mt-10) REVERT: C 138 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8110 (tttt) REVERT: C 148 LYS cc_start: 0.8379 (mppt) cc_final: 0.7830 (mmtt) outliers start: 21 outliers final: 4 residues processed: 133 average time/residue: 1.3998 time to fit residues: 196.9241 Evaluate side-chains 123 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 91 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.0370 chunk 86 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 76 optimal weight: 0.0050 chunk 71 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.4272 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.164023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116413 restraints weight = 7419.049| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.68 r_work: 0.3267 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8304 Z= 0.115 Angle : 0.547 6.477 11334 Z= 0.275 Chirality : 0.045 0.179 1302 Planarity : 0.004 0.044 1395 Dihedral : 11.015 89.995 1530 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.78 % Allowed : 18.24 % Favored : 78.99 % 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: 1.20 (0.28), residues: 984 helix: 1.51 (0.35), residues: 273 sheet: 0.47 (0.28), residues: 309 loop : 0.78 (0.35), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 259 HIS 0.002 0.001 HIS B 355 PHE 0.009 0.001 PHE B 243 TYR 0.015 0.001 TYR C 90 ARG 0.007 0.000 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00896 ( 9) link_NAG-ASN : angle 2.28239 ( 27) link_BETA1-4 : bond 0.00545 ( 9) link_BETA1-4 : angle 1.96747 ( 27) hydrogen bonds : bond 0.03031 ( 241) hydrogen bonds : angle 4.50512 ( 606) SS BOND : bond 0.00268 ( 12) SS BOND : angle 1.00687 ( 24) covalent geometry : bond 0.00253 ( 8274) covalent geometry : angle 0.52655 (11256) *********************** 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 142 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.862 Fit side-chains REVERT: A 52 GLU cc_start: 0.7927 (tp30) cc_final: 0.7621 (mt-10) REVERT: A 138 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8273 (tttt) REVERT: A 275 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: A 332 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.5981 (mpm) REVERT: B 197 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7822 (ttm110) REVERT: B 215 LYS cc_start: 0.8316 (tttp) cc_final: 0.7922 (ttmm) REVERT: B 275 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: B 332 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.6162 (mpm) REVERT: C 138 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8124 (tttt) REVERT: C 148 LYS cc_start: 0.8328 (mppt) cc_final: 0.7781 (mmtt) outliers start: 23 outliers final: 7 residues processed: 133 average time/residue: 1.3106 time to fit residues: 184.1867 Evaluate side-chains 128 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 275 GLU 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 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 0 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 83 optimal weight: 0.2980 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.162324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114396 restraints weight = 7354.345| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.67 r_work: 0.3239 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8304 Z= 0.158 Angle : 0.573 7.018 11334 Z= 0.288 Chirality : 0.046 0.170 1302 Planarity : 0.004 0.044 1395 Dihedral : 10.109 88.909 1530 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.62 % Allowed : 17.75 % 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: 1.27 (0.28), residues: 984 helix: 1.66 (0.35), residues: 273 sheet: 0.51 (0.27), residues: 324 loop : 0.75 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 9) link_NAG-ASN : angle 2.36577 ( 27) link_BETA1-4 : bond 0.00504 ( 9) link_BETA1-4 : angle 1.86759 ( 27) hydrogen bonds : bond 0.03085 ( 241) hydrogen bonds : angle 4.55867 ( 606) SS BOND : bond 0.00306 ( 12) SS BOND : angle 1.14359 ( 24) covalent geometry : bond 0.00355 ( 8274) covalent geometry : angle 0.55319 (11256) *********************** 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 147 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.857 Fit side-chains REVERT: A 138 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8293 (tttt) REVERT: A 275 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: A 332 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.6019 (mpm) REVERT: B 138 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8192 (tttt) REVERT: B 197 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.7910 (ttm110) REVERT: B 215 LYS cc_start: 0.8365 (tttp) cc_final: 0.7982 (ttmm) REVERT: B 275 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: B 332 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.6223 (mpm) REVERT: C 52 GLU cc_start: 0.7974 (tp30) cc_final: 0.7557 (mt-10) REVERT: C 138 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8199 (tttt) REVERT: C 148 LYS cc_start: 0.8328 (mppt) cc_final: 0.7761 (mmtt) REVERT: C 332 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.6092 (mpm) outliers start: 30 outliers final: 11 residues processed: 136 average time/residue: 1.4679 time to fit residues: 210.3771 Evaluate side-chains 133 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 275 GLU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 33 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115009 restraints weight = 7359.644| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.67 r_work: 0.3243 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8304 Z= 0.146 Angle : 0.552 7.315 11334 Z= 0.279 Chirality : 0.045 0.145 1302 Planarity : 0.004 0.044 1395 Dihedral : 9.616 88.614 1530 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.50 % Allowed : 17.51 % Favored : 78.99 % 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 (0.28), residues: 984 helix: 1.67 (0.35), residues: 273 sheet: 0.52 (0.27), residues: 324 loop : 0.78 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 9) link_NAG-ASN : angle 2.39057 ( 27) link_BETA1-4 : bond 0.00483 ( 9) link_BETA1-4 : angle 1.76096 ( 27) hydrogen bonds : bond 0.02982 ( 241) hydrogen bonds : angle 4.51930 ( 606) SS BOND : bond 0.00296 ( 12) SS BOND : angle 1.13279 ( 24) covalent geometry : bond 0.00328 ( 8274) covalent geometry : angle 0.53194 (11256) *********************** 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 145 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.862 Fit side-chains REVERT: A 138 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8325 (tttt) REVERT: A 275 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: A 332 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.6060 (mpm) REVERT: B 138 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8222 (tttt) REVERT: B 215 LYS cc_start: 0.8391 (tttp) cc_final: 0.8028 (ttmm) REVERT: B 267 VAL cc_start: 0.7915 (m) cc_final: 0.7597 (p) REVERT: B 275 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: B 332 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.6308 (mpm) REVERT: C 52 GLU cc_start: 0.7996 (tp30) cc_final: 0.7586 (mt-10) REVERT: C 138 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8237 (tttt) REVERT: C 148 LYS cc_start: 0.8354 (mppt) cc_final: 0.7790 (mmtt) REVERT: C 332 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.6117 (mpm) outliers start: 29 outliers final: 12 residues processed: 135 average time/residue: 1.4843 time to fit residues: 210.9042 Evaluate side-chains 137 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 332 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.7317 > 50: distance: 95 - 151: 34.775 distance: 101 - 108: 35.935 distance: 108 - 109: 39.462 distance: 109 - 110: 40.169 distance: 109 - 112: 55.735 distance: 110 - 111: 57.022 distance: 110 - 118: 40.492 distance: 111 - 136: 3.208 distance: 112 - 113: 56.868 distance: 113 - 114: 70.142 distance: 113 - 115: 59.005 distance: 114 - 116: 55.732 distance: 115 - 117: 17.389 distance: 116 - 117: 69.641 distance: 119 - 120: 69.843 distance: 120 - 121: 40.724 distance: 120 - 125: 68.719 distance: 121 - 146: 3.107 distance: 125 - 126: 69.510 distance: 126 - 127: 67.835 distance: 127 - 128: 69.717 distance: 127 - 136: 70.056 distance: 129 - 130: 41.239 distance: 130 - 131: 42.827 distance: 131 - 132: 54.664 distance: 133 - 134: 40.590 distance: 133 - 135: 39.411 distance: 136 - 137: 39.492 distance: 137 - 138: 68.540 distance: 137 - 140: 40.046 distance: 138 - 139: 40.001 distance: 138 - 146: 39.918 distance: 140 - 141: 56.936 distance: 141 - 142: 39.393 distance: 141 - 143: 57.259 distance: 142 - 144: 39.852 distance: 143 - 145: 58.515 distance: 144 - 145: 11.382 distance: 146 - 147: 68.616 distance: 147 - 148: 42.944 distance: 147 - 150: 55.207 distance: 148 - 149: 62.744 distance: 148 - 152: 25.559 distance: 150 - 151: 39.660 distance: 152 - 153: 38.914 distance: 153 - 154: 40.244 distance: 153 - 156: 40.266 distance: 154 - 155: 56.140 distance: 154 - 163: 55.451 distance: 156 - 157: 40.649 distance: 157 - 158: 39.219 distance: 158 - 159: 39.285 distance: 159 - 160: 40.020 distance: 160 - 161: 69.569 distance: 163 - 164: 40.297 distance: 163 - 169: 70.577 distance: 164 - 165: 68.158 distance: 164 - 167: 68.786 distance: 165 - 166: 57.718 distance: 165 - 170: 40.519 distance: 167 - 168: 56.071 distance: 168 - 169: 41.019 distance: 170 - 171: 39.545 distance: 171 - 172: 57.052 distance: 171 - 174: 56.105 distance: 172 - 173: 57.098 distance: 172 - 178: 56.854 distance: 174 - 175: 57.971 distance: 174 - 176: 57.265 distance: 175 - 177: 57.497 distance: 179 - 180: 57.610 distance: 179 - 182: 39.741 distance: 180 - 181: 56.347 distance: 180 - 190: 56.668 distance: 182 - 183: 55.323 distance: 183 - 185: 57.885 distance: 184 - 186: 39.427 distance: 185 - 187: 69.274 distance: 187 - 188: 55.285 distance: 188 - 189: 57.749 distance: 190 - 191: 56.802 distance: 191 - 192: 41.097 distance: 191 - 194: 55.079 distance: 192 - 193: 55.399 distance: 192 - 199: 35.628 distance: 194 - 195: 39.262 distance: 196 - 197: 39.946 distance: 196 - 198: 69.230