Starting phenix.real_space_refine on Thu Jul 2 07:18:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vc0_64938/07_2026/9vc0_64938.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vc0_64938/07_2026/9vc0_64938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vc0_64938/07_2026/9vc0_64938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vc0_64938/07_2026/9vc0_64938.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vc0_64938/07_2026/9vc0_64938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vc0_64938/07_2026/9vc0_64938.map" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.094 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 Mn 4 7.51 5 C 4656 2.51 5 N 1196 2.21 5 O 1510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7370 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1805 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Chain: "B" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1805 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Chain: "D" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1805 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Chain: "C" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1805 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Chain: "a" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BMA': 1, 'MAN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BMA': 1, 'MAN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BMA': 1, 'MAN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BMA': 1, 'MAN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Chain breaks: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 1.19, per 1000 atoms: 0.16 Number of scatterers: 7370 At special positions: 0 Unit cell: (87.48, 81, 79.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 4 24.99 Ca 4 19.99 O 1510 8.00 N 1196 7.00 C 4656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 ALPHA1-3 " BMA a 1 " - " MAN a 2 " " BMA b 1 " - " MAN b 2 " " BMA c 1 " - " MAN c 2 " " BMA d 1 " - " MAN d 2 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 317.2 milliseconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 12 sheets defined 4.3% alpha, 55.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.876A pdb=" N PHE A 105 " --> pdb=" O HIS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.875A pdb=" N PHE B 105 " --> pdb=" O HIS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.876A pdb=" N PHE D 105 " --> pdb=" O HIS D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 214 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.876A pdb=" N PHE C 105 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 214 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 208 removed outlier: 6.335A pdb=" N ALA A 63 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR A 247 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 65 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU A 245 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER A 67 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER A 243 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP A 69 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE A 241 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE A 71 " --> pdb=" O TRP A 239 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TRP A 239 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN A 73 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN B 73 " --> pdb=" O HIS B 237 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TRP B 239 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 71 " --> pdb=" O TRP B 239 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE B 241 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP B 69 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER B 243 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER B 67 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU B 245 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU B 65 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR B 247 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA B 63 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 22 removed outlier: 5.239A pdb=" N VAL A 221 " --> pdb=" O TYR A 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 18 through 22 removed outlier: 5.239A pdb=" N VAL A 221 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 87 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL A 166 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 22 removed outlier: 5.238A pdb=" N VAL B 221 " --> pdb=" O TYR B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 22 removed outlier: 5.238A pdb=" N VAL B 221 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 87 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL B 166 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 31 through 32 Processing sheet with id=AA8, first strand: chain 'D' and resid 203 through 208 removed outlier: 6.334A pdb=" N ALA D 63 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR D 247 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU D 65 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU D 245 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER D 67 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER D 243 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP D 69 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE D 241 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE D 71 " --> pdb=" O TRP D 239 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TRP D 239 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN D 73 " --> pdb=" O HIS D 237 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN C 73 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TRP C 239 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE C 71 " --> pdb=" O TRP C 239 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE C 241 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP C 69 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER C 243 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER C 67 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU C 245 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU C 65 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR C 247 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 63 " --> pdb=" O THR C 247 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 18 through 22 removed outlier: 5.239A pdb=" N VAL D 221 " --> pdb=" O TYR D 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 18 through 22 removed outlier: 5.239A pdb=" N VAL D 221 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY D 87 " --> pdb=" O SER D 226 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL D 166 " --> pdb=" O ILE D 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 18 through 22 removed outlier: 5.238A pdb=" N VAL C 221 " --> pdb=" O TYR C 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 18 through 22 removed outlier: 5.238A pdb=" N VAL C 221 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY C 87 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL C 166 " --> pdb=" O ILE C 157 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1008 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: 0.84 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 1176 1.29 - 1.36: 1156 1.36 - 1.42: 967 1.42 - 1.49: 1214 1.49 - 1.55: 2999 Bond restraints: 7512 Sorted by residual: bond pdb=" N ILE A 162 " pdb=" CA ILE A 162 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.17e-02 7.31e+03 6.39e+00 bond pdb=" N SER B 164 " pdb=" CA SER B 164 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 5.93e+00 bond pdb=" C1 BMA b 1 " pdb=" O1 BMA b 1 " ideal model delta sigma weight residual 1.383 1.432 -0.049 2.00e-02 2.50e+03 5.92e+00 bond pdb=" C1 BMA c 1 " pdb=" O1 BMA c 1 " ideal model delta sigma weight residual 1.383 1.432 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C1 BMA a 1 " pdb=" O1 BMA a 1 " ideal model delta sigma weight residual 1.383 1.431 -0.048 2.00e-02 2.50e+03 5.76e+00 ... (remaining 7507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 9548 1.36 - 2.71: 562 2.71 - 4.07: 117 4.07 - 5.42: 33 5.42 - 6.78: 16 Bond angle restraints: 10276 Sorted by residual: angle pdb=" N ILE A 162 " pdb=" CA ILE A 162 " pdb=" C ILE A 162 " ideal model delta sigma weight residual 113.07 107.98 5.09 1.36e+00 5.41e-01 1.40e+01 angle pdb=" C ALA B 85 " pdb=" N ASP B 86 " pdb=" CA ASP B 86 " ideal model delta sigma weight residual 121.70 127.24 -5.54 1.80e+00 3.09e-01 9.48e+00 angle pdb=" C ALA A 85 " pdb=" N ASP A 86 " pdb=" CA ASP A 86 " ideal model delta sigma weight residual 121.70 127.17 -5.47 1.80e+00 3.09e-01 9.24e+00 angle pdb=" C ALA D 85 " pdb=" N ASP D 86 " pdb=" CA ASP D 86 " ideal model delta sigma weight residual 121.70 127.17 -5.47 1.80e+00 3.09e-01 9.23e+00 angle pdb=" C ALA C 85 " pdb=" N ASP C 86 " pdb=" CA ASP C 86 " ideal model delta sigma weight residual 121.70 127.15 -5.45 1.80e+00 3.09e-01 9.17e+00 ... (remaining 10271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 4176 21.55 - 43.09: 215 43.09 - 64.64: 25 64.64 - 86.19: 32 86.19 - 107.74: 16 Dihedral angle restraints: 4464 sinusoidal: 1764 harmonic: 2700 Sorted by residual: dihedral pdb=" CA ALA C 89 " pdb=" C ALA C 89 " pdb=" N PHE C 90 " pdb=" CA PHE C 90 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA D 89 " pdb=" C ALA D 89 " pdb=" N PHE D 90 " pdb=" CA PHE D 90 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA A 89 " pdb=" C ALA A 89 " pdb=" N PHE A 90 " pdb=" CA PHE A 90 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 4461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 743 0.047 - 0.094: 306 0.094 - 0.140: 108 0.140 - 0.187: 18 0.187 - 0.234: 9 Chirality restraints: 1184 Sorted by residual: chirality pdb=" C3 BMA d 1 " pdb=" C2 BMA d 1 " pdb=" C4 BMA d 1 " pdb=" O3 BMA d 1 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C3 BMA c 1 " pdb=" C2 BMA c 1 " pdb=" C4 BMA c 1 " pdb=" O3 BMA c 1 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C3 BMA a 1 " pdb=" C2 BMA a 1 " pdb=" C4 BMA a 1 " pdb=" O3 BMA a 1 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1181 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 93 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO D 94 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 94 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 94 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 93 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO A 94 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 93 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO C 94 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 94 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 94 " 0.026 5.00e-02 4.00e+02 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 76 2.59 - 3.17: 5629 3.17 - 3.74: 12079 3.74 - 4.32: 18596 4.32 - 4.90: 30138 Nonbonded interactions: 66518 Sorted by model distance: nonbonded pdb=" OE2 GLU C 138 " pdb="MN MN C 302 " model vdw 2.012 3.060 nonbonded pdb=" OE2 GLU B 138 " pdb="MN MN B 302 " model vdw 2.022 3.060 nonbonded pdb=" OE2 GLU A 138 " pdb="MN MN A 302 " model vdw 2.024 3.060 nonbonded pdb=" OE2 GLU D 138 " pdb="MN MN D 302 " model vdw 2.069 3.060 nonbonded pdb=" NE2 HIS A 154 " pdb="MN MN A 302 " model vdw 2.215 3.140 ... (remaining 66513 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 1.810 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.030 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:5.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 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 : 0.005 0.049 7516 Z= 0.238 Angle : 0.794 6.778 10288 Z= 0.431 Chirality : 0.057 0.234 1184 Planarity : 0.007 0.047 1296 Dihedral : 16.953 107.736 2720 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.25), residues: 908 helix: None (None), residues: 0 sheet: 0.39 (0.25), residues: 372 loop : -1.41 (0.22), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 220 TYR 0.008 0.002 TYR A 52 PHE 0.020 0.003 PHE A 241 TRP 0.008 0.001 TRP D 59 HIS 0.004 0.001 HIS C 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.24 ( 7512) covalent geometry : angle 0.79399 / 0.43 (10276) hydrogen bonds : bond 0.23229 / 14.91 ( 304) hydrogen bonds : angle 9.02724 / 6.16 ( 1008) link_ALPHA1-3 : bond 0.00482 / 0.22 ( 4) link_ALPHA1-3 : angle 0.98932 / 0.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.214 Fit side-chains REVERT: A 41 ASN cc_start: 0.8557 (m-40) cc_final: 0.8319 (m-40) REVERT: A 231 LYS cc_start: 0.8243 (ptpp) cc_final: 0.8002 (pttt) REVERT: B 41 ASN cc_start: 0.8594 (m-40) cc_final: 0.8333 (m-40) REVERT: B 231 LYS cc_start: 0.8260 (ptpp) cc_final: 0.8024 (pttt) REVERT: D 41 ASN cc_start: 0.8700 (m-40) cc_final: 0.8421 (m-40) REVERT: D 231 LYS cc_start: 0.8239 (ptpp) cc_final: 0.7977 (pttt) REVERT: C 41 ASN cc_start: 0.8508 (m-40) cc_final: 0.8275 (m-40) REVERT: C 231 LYS cc_start: 0.8171 (ptpp) cc_final: 0.7868 (pttt) outliers start: 0 outliers final: 1 residues processed: 139 average time/residue: 0.5126 time to fit residues: 74.9333 Evaluate side-chains 125 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0370 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 23 HIS A 73 ASN A 113 ASN A 160 ASN A 173 GLN A 234 ASN B 14 ASN B 23 HIS B 73 ASN B 113 ASN B 160 ASN B 173 GLN B 234 ASN D 14 ASN D 23 HIS D 73 ASN D 113 ASN D 160 ASN D 173 GLN D 234 ASN C 14 ASN C 23 HIS C 73 ASN C 113 ASN C 160 ASN C 173 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117101 restraints weight = 7834.144| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.64 r_work: 0.3388 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7516 Z= 0.139 Angle : 0.587 4.506 10288 Z= 0.325 Chirality : 0.047 0.169 1184 Planarity : 0.005 0.040 1296 Dihedral : 13.079 71.418 1150 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.50 % Allowed : 7.67 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.26), residues: 908 helix: None (None), residues: 0 sheet: 0.44 (0.28), residues: 344 loop : -0.76 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.008 0.001 TYR A 52 PHE 0.015 0.002 PHE C 68 TRP 0.004 0.001 TRP D 59 HIS 0.002 0.000 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 7512) covalent geometry : angle 0.58425 / 0.32 (10276) hydrogen bonds : bond 0.05198 / 3.38 ( 304) hydrogen bonds : angle 5.68029 / 3.90 ( 1008) link_ALPHA1-3 : bond 0.00560 / 0.26 ( 4) link_ALPHA1-3 : angle 1.83973 / 1.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.197 Fit side-chains REVERT: A 41 ASN cc_start: 0.8692 (m-40) cc_final: 0.8400 (m-40) REVERT: A 149 ASP cc_start: 0.7019 (m-30) cc_final: 0.6778 (m-30) REVERT: A 231 LYS cc_start: 0.8370 (ptpp) cc_final: 0.8161 (pttt) REVERT: B 41 ASN cc_start: 0.8700 (m-40) cc_final: 0.8401 (m-40) REVERT: B 86 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8424 (m-30) REVERT: B 149 ASP cc_start: 0.7020 (m-30) cc_final: 0.6795 (m-30) REVERT: B 231 LYS cc_start: 0.8382 (ptpp) cc_final: 0.8173 (pttt) REVERT: D 41 ASN cc_start: 0.8737 (m-40) cc_final: 0.8400 (m-40) REVERT: D 149 ASP cc_start: 0.7389 (m-30) cc_final: 0.7105 (m-30) REVERT: D 231 LYS cc_start: 0.8421 (ptpp) cc_final: 0.8158 (pttt) REVERT: C 86 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8462 (m-30) REVERT: C 231 LYS cc_start: 0.8354 (ptpp) cc_final: 0.8085 (pttt) outliers start: 4 outliers final: 1 residues processed: 127 average time/residue: 0.5497 time to fit residues: 73.0403 Evaluate side-chains 116 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 86 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN B 133 ASN D 133 ASN C 28 ASN C 133 ASN C 234 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.134698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115658 restraints weight = 7977.367| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.67 r_work: 0.3368 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7516 Z= 0.150 Angle : 0.567 4.612 10288 Z= 0.307 Chirality : 0.046 0.157 1184 Planarity : 0.005 0.063 1296 Dihedral : 9.964 49.481 1148 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.73 % Allowed : 9.53 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.27), residues: 908 helix: None (None), residues: 0 sheet: 0.51 (0.27), residues: 376 loop : -0.62 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 233 TYR 0.011 0.001 TYR C 52 PHE 0.015 0.002 PHE C 68 TRP 0.004 0.001 TRP D 59 HIS 0.003 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 7512) covalent geometry : angle 0.56434 / 0.31 (10276) hydrogen bonds : bond 0.04568 / 2.98 ( 304) hydrogen bonds : angle 5.18168 / 3.53 ( 1008) link_ALPHA1-3 : bond 0.00691 / 0.31 ( 4) link_ALPHA1-3 : angle 1.76414 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.274 Fit side-chains REVERT: A 41 ASN cc_start: 0.8806 (m-40) cc_final: 0.8477 (m-40) REVERT: A 138 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8683 (pt0) REVERT: A 231 LYS cc_start: 0.8403 (ptpp) cc_final: 0.8185 (pttt) REVERT: B 41 ASN cc_start: 0.8794 (m-40) cc_final: 0.8486 (m-40) REVERT: B 86 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8496 (m-30) REVERT: B 138 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8708 (pt0) REVERT: B 231 LYS cc_start: 0.8430 (ptpp) cc_final: 0.8216 (pttt) REVERT: D 41 ASN cc_start: 0.8802 (m-40) cc_final: 0.8458 (m-40) REVERT: D 86 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8457 (m-30) REVERT: D 88 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8466 (tt) REVERT: D 231 LYS cc_start: 0.8452 (ptpp) cc_final: 0.8213 (pttt) REVERT: C 41 ASN cc_start: 0.8687 (m-40) cc_final: 0.8340 (m-40) REVERT: C 86 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8448 (m-30) REVERT: C 138 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8687 (pt0) REVERT: C 231 LYS cc_start: 0.8392 (ptpp) cc_final: 0.8134 (pttt) outliers start: 14 outliers final: 4 residues processed: 126 average time/residue: 0.5392 time to fit residues: 71.2160 Evaluate side-chains 125 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 138 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 60 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 234 ASN D 234 ASN C 28 ASN C 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109363 restraints weight = 8226.940| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.73 r_work: 0.3292 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 7516 Z= 0.312 Angle : 0.675 7.040 10288 Z= 0.364 Chirality : 0.051 0.169 1184 Planarity : 0.006 0.047 1296 Dihedral : 9.080 38.022 1148 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.48 % Allowed : 9.53 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.27), residues: 908 helix: None (None), residues: 0 sheet: 0.71 (0.27), residues: 376 loop : -0.59 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 190 TYR 0.015 0.002 TYR C 52 PHE 0.017 0.003 PHE D 68 TRP 0.006 0.002 TRP A 246 HIS 0.004 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.31 ( 7512) covalent geometry : angle 0.67200 / 0.36 (10276) hydrogen bonds : bond 0.05337 / 3.49 ( 304) hydrogen bonds : angle 5.70234 / 3.88 ( 1008) link_ALPHA1-3 : bond 0.00375 / 0.17 ( 4) link_ALPHA1-3 : angle 1.95622 / 1.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.200 Fit side-chains REVERT: A 231 LYS cc_start: 0.8510 (ptpp) cc_final: 0.8252 (pttt) REVERT: B 86 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8549 (m-30) REVERT: B 88 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8452 (tt) REVERT: B 231 LYS cc_start: 0.8536 (ptpp) cc_final: 0.8283 (pttt) REVERT: D 86 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8525 (m-30) REVERT: D 138 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8746 (pt0) REVERT: D 231 LYS cc_start: 0.8537 (ptpp) cc_final: 0.8284 (pttt) REVERT: C 86 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8555 (m-30) REVERT: C 88 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8417 (tt) REVERT: C 138 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8748 (pt0) REVERT: C 231 LYS cc_start: 0.8518 (ptpp) cc_final: 0.8255 (pttt) outliers start: 20 outliers final: 10 residues processed: 125 average time/residue: 0.5465 time to fit residues: 71.4272 Evaluate side-chains 124 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 138 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 234 ASN D 234 ASN C 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.133032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113862 restraints weight = 8120.699| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.68 r_work: 0.3349 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7516 Z= 0.155 Angle : 0.566 4.865 10288 Z= 0.308 Chirality : 0.046 0.156 1184 Planarity : 0.006 0.072 1296 Dihedral : 7.703 38.740 1148 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.23 % Allowed : 10.15 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.27), residues: 908 helix: None (None), residues: 0 sheet: 0.65 (0.27), residues: 376 loop : -0.52 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 190 TYR 0.009 0.001 TYR A 52 PHE 0.015 0.002 PHE B 68 TRP 0.004 0.001 TRP D 59 HIS 0.003 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 7512) covalent geometry : angle 0.56294 / 0.31 (10276) hydrogen bonds : bond 0.04363 / 2.85 ( 304) hydrogen bonds : angle 5.30154 / 3.62 ( 1008) link_ALPHA1-3 : bond 0.00618 / 0.29 ( 4) link_ALPHA1-3 : angle 1.79467 / 1.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.177 Fit side-chains REVERT: A 138 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8682 (pt0) REVERT: A 229 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: A 231 LYS cc_start: 0.8482 (ptpp) cc_final: 0.8239 (pttt) REVERT: B 86 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8516 (m-30) REVERT: B 88 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8518 (tt) REVERT: B 138 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8703 (pt0) REVERT: B 231 LYS cc_start: 0.8500 (ptpp) cc_final: 0.8255 (pttt) REVERT: D 41 ASN cc_start: 0.8872 (m-40) cc_final: 0.8562 (m-40) REVERT: D 86 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8497 (m-30) REVERT: D 88 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8494 (tt) REVERT: D 138 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8716 (pt0) REVERT: D 231 LYS cc_start: 0.8500 (ptpp) cc_final: 0.8254 (pttt) REVERT: C 86 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8515 (m-30) REVERT: C 88 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8490 (tt) REVERT: C 138 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8701 (pt0) REVERT: C 231 LYS cc_start: 0.8454 (ptpp) cc_final: 0.8207 (pttt) outliers start: 18 outliers final: 5 residues processed: 130 average time/residue: 0.5377 time to fit residues: 73.2768 Evaluate side-chains 132 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 138 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 78 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 66 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.136993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117133 restraints weight = 8266.604| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.74 r_work: 0.3378 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7516 Z= 0.121 Angle : 0.523 4.038 10288 Z= 0.285 Chirality : 0.045 0.150 1184 Planarity : 0.006 0.088 1296 Dihedral : 6.708 38.311 1148 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.61 % Allowed : 10.52 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.28), residues: 908 helix: None (None), residues: 0 sheet: 0.61 (0.27), residues: 376 loop : -0.47 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 190 TYR 0.008 0.001 TYR B 52 PHE 0.014 0.002 PHE D 68 TRP 0.004 0.001 TRP D 59 HIS 0.002 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 7512) covalent geometry : angle 0.52045 / 0.29 (10276) hydrogen bonds : bond 0.03843 / 2.50 ( 304) hydrogen bonds : angle 5.02982 / 3.44 ( 1008) link_ALPHA1-3 : bond 0.00622 / 0.28 ( 4) link_ALPHA1-3 : angle 1.57969 / 1.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.183 Fit side-chains REVERT: A 41 ASN cc_start: 0.8830 (m-40) cc_final: 0.8527 (m-40) REVERT: A 138 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8686 (pt0) REVERT: A 231 LYS cc_start: 0.8433 (ptpp) cc_final: 0.8230 (pttt) REVERT: B 41 ASN cc_start: 0.8863 (m-40) cc_final: 0.8561 (m-40) REVERT: B 138 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8695 (pt0) REVERT: B 231 LYS cc_start: 0.8443 (ptpp) cc_final: 0.8242 (pttt) REVERT: D 41 ASN cc_start: 0.8851 (m-40) cc_final: 0.8511 (m-40) REVERT: D 138 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8725 (pt0) REVERT: D 231 LYS cc_start: 0.8457 (ptpp) cc_final: 0.8252 (pttt) REVERT: C 41 ASN cc_start: 0.8826 (m-40) cc_final: 0.8472 (m-40) REVERT: C 138 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8693 (pt0) REVERT: C 149 ASP cc_start: 0.7459 (m-30) cc_final: 0.7231 (m-30) REVERT: C 231 LYS cc_start: 0.8426 (ptpp) cc_final: 0.8208 (pttt) outliers start: 13 outliers final: 5 residues processed: 126 average time/residue: 0.5293 time to fit residues: 69.8566 Evaluate side-chains 123 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 138 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 40 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 78 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN C 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118043 restraints weight = 7971.857| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.67 r_work: 0.3391 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7516 Z= 0.111 Angle : 0.507 4.105 10288 Z= 0.277 Chirality : 0.044 0.147 1184 Planarity : 0.006 0.095 1296 Dihedral : 6.242 35.575 1148 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.10 % Allowed : 10.27 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.28), residues: 908 helix: None (None), residues: 0 sheet: 0.61 (0.28), residues: 376 loop : -0.46 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.008 0.001 TYR B 52 PHE 0.014 0.002 PHE D 68 TRP 0.004 0.001 TRP C 59 HIS 0.002 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 7512) covalent geometry : angle 0.50494 / 0.28 (10276) hydrogen bonds : bond 0.03635 / 2.36 ( 304) hydrogen bonds : angle 4.90727 / 3.35 ( 1008) link_ALPHA1-3 : bond 0.00550 / 0.24 ( 4) link_ALPHA1-3 : angle 1.49456 / 0.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.176 Fit side-chains REVERT: A 41 ASN cc_start: 0.8826 (m-40) cc_final: 0.8533 (m-40) REVERT: A 138 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8659 (pt0) REVERT: A 231 LYS cc_start: 0.8357 (ptpp) cc_final: 0.8100 (pttt) REVERT: B 41 ASN cc_start: 0.8839 (m-40) cc_final: 0.8542 (m-40) REVERT: B 138 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8661 (pt0) REVERT: D 41 ASN cc_start: 0.8849 (m-40) cc_final: 0.8507 (m-40) REVERT: D 138 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8706 (pt0) REVERT: D 231 LYS cc_start: 0.8403 (ptpp) cc_final: 0.8128 (pttt) REVERT: C 41 ASN cc_start: 0.8826 (m-40) cc_final: 0.8528 (m-40) REVERT: C 138 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8670 (pt0) outliers start: 17 outliers final: 7 residues processed: 130 average time/residue: 0.5674 time to fit residues: 77.3028 Evaluate side-chains 124 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 138 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 25 optimal weight: 0.0270 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 28 ASN D 133 ASN C 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.135112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115722 restraints weight = 8089.038| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.70 r_work: 0.3370 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7516 Z= 0.141 Angle : 0.525 4.598 10288 Z= 0.287 Chirality : 0.045 0.152 1184 Planarity : 0.006 0.094 1296 Dihedral : 6.015 31.662 1148 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.72 % Allowed : 10.02 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.28), residues: 908 helix: None (None), residues: 0 sheet: 0.64 (0.27), residues: 376 loop : -0.46 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 190 TYR 0.010 0.001 TYR A 52 PHE 0.015 0.002 PHE C 68 TRP 0.005 0.001 TRP B 59 HIS 0.003 0.001 HIS D 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7512) covalent geometry : angle 0.52310 / 0.29 (10276) hydrogen bonds : bond 0.03854 / 2.50 ( 304) hydrogen bonds : angle 4.96280 / 3.39 ( 1008) link_ALPHA1-3 : bond 0.00456 / 0.21 ( 4) link_ALPHA1-3 : angle 1.50583 / 0.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.245 Fit side-chains REVERT: A 41 ASN cc_start: 0.8804 (m-40) cc_final: 0.8502 (m-40) REVERT: A 138 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8691 (pt0) REVERT: A 229 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: B 41 ASN cc_start: 0.8809 (m-40) cc_final: 0.8496 (m-40) REVERT: B 86 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8476 (m-30) REVERT: B 138 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8692 (pt0) REVERT: D 41 ASN cc_start: 0.8867 (m-40) cc_final: 0.8526 (m-40) REVERT: D 88 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8502 (tt) REVERT: D 138 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8705 (pt0) REVERT: C 41 ASN cc_start: 0.8836 (m-40) cc_final: 0.8532 (m-40) REVERT: C 138 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8683 (pt0) outliers start: 22 outliers final: 13 residues processed: 131 average time/residue: 0.5184 time to fit residues: 71.1747 Evaluate side-chains 132 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 231 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115100 restraints weight = 7988.616| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.69 r_work: 0.3361 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7516 Z= 0.150 Angle : 0.535 4.863 10288 Z= 0.293 Chirality : 0.045 0.155 1184 Planarity : 0.006 0.092 1296 Dihedral : 5.754 24.315 1148 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.09 % Allowed : 10.02 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.27), residues: 908 helix: None (None), residues: 0 sheet: 0.66 (0.27), residues: 376 loop : -0.47 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 190 TYR 0.010 0.001 TYR A 52 PHE 0.015 0.002 PHE D 68 TRP 0.005 0.001 TRP B 59 HIS 0.003 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 7512) covalent geometry : angle 0.53239 / 0.29 (10276) hydrogen bonds : bond 0.03968 / 2.58 ( 304) hydrogen bonds : angle 5.03588 / 3.43 ( 1008) link_ALPHA1-3 : bond 0.00355 / 0.17 ( 4) link_ALPHA1-3 : angle 1.54389 / 1.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.254 Fit side-chains REVERT: A 41 ASN cc_start: 0.8857 (m-40) cc_final: 0.8547 (m-40) REVERT: A 88 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8298 (tt) REVERT: A 138 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8686 (pt0) REVERT: A 190 ARG cc_start: 0.8413 (mmt-90) cc_final: 0.8059 (mmt-90) REVERT: A 229 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: B 41 ASN cc_start: 0.8859 (m-40) cc_final: 0.8546 (m-40) REVERT: B 88 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8515 (tt) REVERT: B 138 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8671 (pt0) REVERT: B 208 ASP cc_start: 0.7648 (m-30) cc_final: 0.7392 (m-30) REVERT: D 41 ASN cc_start: 0.8834 (m-40) cc_final: 0.8508 (m-40) REVERT: D 88 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8500 (tt) REVERT: D 138 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8694 (pt0) REVERT: C 41 ASN cc_start: 0.8849 (m-40) cc_final: 0.8544 (m-40) REVERT: C 138 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8675 (pt0) outliers start: 25 outliers final: 13 residues processed: 135 average time/residue: 0.4906 time to fit residues: 69.6652 Evaluate side-chains 137 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 231 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 13 optimal weight: 0.0970 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.115015 restraints weight = 8019.198| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.69 r_work: 0.3361 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7516 Z= 0.154 Angle : 0.539 4.873 10288 Z= 0.296 Chirality : 0.045 0.153 1184 Planarity : 0.005 0.076 1296 Dihedral : 5.523 15.654 1148 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.97 % Allowed : 9.90 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.28), residues: 908 helix: None (None), residues: 0 sheet: 0.67 (0.27), residues: 376 loop : -0.46 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 190 TYR 0.010 0.001 TYR A 52 PHE 0.015 0.002 PHE A 68 TRP 0.005 0.001 TRP B 59 HIS 0.003 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 7512) covalent geometry : angle 0.53713 / 0.30 (10276) hydrogen bonds : bond 0.03985 / 2.59 ( 304) hydrogen bonds : angle 5.05534 / 3.45 ( 1008) link_ALPHA1-3 : bond 0.00321 / 0.15 ( 4) link_ALPHA1-3 : angle 1.55426 / 1.01 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.275 Fit side-chains REVERT: A 41 ASN cc_start: 0.8852 (m-40) cc_final: 0.8542 (m-40) REVERT: A 88 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8288 (tt) REVERT: A 138 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8682 (pt0) REVERT: B 41 ASN cc_start: 0.8857 (m-40) cc_final: 0.8558 (m-40) REVERT: B 86 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8493 (m-30) REVERT: B 88 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8517 (tt) REVERT: D 41 ASN cc_start: 0.8856 (m-40) cc_final: 0.8545 (m-40) REVERT: D 86 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8508 (m-30) REVERT: D 88 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8499 (tt) REVERT: D 138 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8684 (pt0) REVERT: C 41 ASN cc_start: 0.8858 (m-40) cc_final: 0.8557 (m-40) REVERT: C 138 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8676 (pt0) outliers start: 24 outliers final: 15 residues processed: 133 average time/residue: 0.4787 time to fit residues: 66.8865 Evaluate side-chains 140 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 231 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 47 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.136513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117736 restraints weight = 8053.590| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.65 r_work: 0.3388 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7516 Z= 0.122 Angle : 0.515 4.050 10288 Z= 0.283 Chirality : 0.045 0.149 1184 Planarity : 0.005 0.077 1296 Dihedral : 5.256 15.684 1148 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.97 % Allowed : 9.90 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.28), residues: 908 helix: None (None), residues: 0 sheet: 0.68 (0.28), residues: 376 loop : -0.46 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 190 TYR 0.009 0.001 TYR B 52 PHE 0.015 0.002 PHE A 68 TRP 0.004 0.001 TRP B 59 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7512) covalent geometry : angle 0.51272 / 0.28 (10276) hydrogen bonds : bond 0.03711 / 2.42 ( 304) hydrogen bonds : angle 4.92324 / 3.35 ( 1008) link_ALPHA1-3 : bond 0.00303 / 0.14 ( 4) link_ALPHA1-3 : angle 1.48027 / 0.96 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2258.34 seconds wall clock time: 39 minutes 16.92 seconds (2356.92 seconds total)