Starting phenix.real_space_refine on Sun Apr 5 02:33:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vbz_64937/04_2026/9vbz_64937.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vbz_64937/04_2026/9vbz_64937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vbz_64937/04_2026/9vbz_64937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vbz_64937/04_2026/9vbz_64937.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vbz_64937/04_2026/9vbz_64937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vbz_64937/04_2026/9vbz_64937.map" } resolution = 2.56 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= 0.001 sd= 0.093 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 4664 2.51 5 N 1196 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7398 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1806 Classifications: {'peptide': 233} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1806 Classifications: {'peptide': 233} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 220} Chain breaks: 1 Chain: "D" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1806 Classifications: {'peptide': 233} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 220} Chain breaks: 1 Chain: "C" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1806 Classifications: {'peptide': 233} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 220} Chain breaks: 1 Chain: "b" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BMA': 1, 'MAN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BMA': 1, 'MAN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BMA': 1, 'MAN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BMA': 1, 'MAN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' MN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' MN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' MN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' MN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 1.75, per 1000 atoms: 0.24 Number of scatterers: 7398 At special positions: 0 Unit cell: (81.648, 87.48, 81, 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 1530 8.00 N 1196 7.00 C 4664 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 ALPHA1-2 " MAN a 2 " - " MAN a 3 " " MAN b 2 " - " MAN b 3 " " MAN c 2 " - " MAN c 3 " " MAN d 2 " - " MAN d 3 " 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: 0.75 Conformation dependent library (CDL) restraints added in 287.3 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1752 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 12 sheets defined 7.7% alpha, 55.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 100 through 106 removed outlier: 3.628A pdb=" N SER A 101B" --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR A 102 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY A 103 " --> pdb=" O GLY A 101A" (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLY A 104 " --> pdb=" O SER A 101B" (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE A 105 " --> pdb=" O THR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.832A pdb=" N PHE B 105 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'D' and resid 100 through 106 removed outlier: 3.717A pdb=" N SER D 101B" --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR D 102 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLY D 103 " --> pdb=" O GLY D 101A" (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY D 104 " --> pdb=" O SER D 101B" (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE D 105 " --> pdb=" O THR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 210 through 214 Processing helix chain 'C' and resid 100 through 106 removed outlier: 3.707A pdb=" N SER C 101B" --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR C 102 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY C 103 " --> pdb=" O GLY C 101A" (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLY C 104 " --> pdb=" O SER C 101B" (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE C 105 " --> pdb=" O THR C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 210 through 214 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 3.509A pdb=" N VAL B 30 " --> pdb=" O THR B 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 208 removed outlier: 6.311A pdb=" N ALA A 63 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR A 247 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 65 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU A 245 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER A 67 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER A 243 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP A 69 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE A 241 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 71 " --> pdb=" O TRP A 239 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TRP A 239 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN A 73 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN B 73 " --> pdb=" O HIS B 237 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP B 239 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 71 " --> pdb=" O TRP B 239 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE B 241 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 69 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER B 243 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER B 67 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU B 245 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 65 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR B 247 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.354A 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: 5.510A 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: 5.510A pdb=" N VAL A 221 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 87 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 4.056A 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: 5.520A 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: 5.520A pdb=" N VAL B 221 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 87 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL B 166 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.530A pdb=" N VAL D 30 " --> pdb=" O THR D 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 203 through 208 removed outlier: 6.326A pdb=" N ALA D 63 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR D 247 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU D 65 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU D 245 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER D 67 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER D 243 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP D 69 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE D 241 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE D 71 " --> pdb=" O TRP D 239 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TRP D 239 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN D 73 " --> pdb=" O HIS D 237 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN C 73 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TRP C 239 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 71 " --> pdb=" O TRP C 239 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C 241 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP C 69 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER C 243 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER C 67 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU C 245 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU C 65 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR C 247 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 6.350A 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: 5.442A 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: 5.442A pdb=" N VAL D 221 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D 87 " --> pdb=" O SER D 226 " (cutoff:3.500A) removed outlier: 4.035A 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: 5.446A 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: 5.446A pdb=" N VAL C 221 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY C 87 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL C 166 " --> pdb=" O ILE C 157 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1035 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: 1.33 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 1184 1.26 - 1.33: 958 1.33 - 1.40: 988 1.40 - 1.48: 1362 1.48 - 1.55: 3056 Bond restraints: 7548 Sorted by residual: bond pdb=" C SER A 188 " pdb=" O SER A 188 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.32e-02 5.74e+03 1.65e+01 bond pdb=" CA SER A 188 " pdb=" CB SER A 188 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.68e-02 3.54e+03 1.18e+01 bond pdb=" C1 BMA d 1 " pdb=" O1 BMA d 1 " ideal model delta sigma weight residual 1.383 1.436 -0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" C1 BMA b 1 " pdb=" O1 BMA b 1 " ideal model delta sigma weight residual 1.383 1.435 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C1 BMA c 1 " pdb=" O1 BMA c 1 " ideal model delta sigma weight residual 1.383 1.435 -0.052 2.00e-02 2.50e+03 6.88e+00 ... (remaining 7543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 9819 1.78 - 3.56: 404 3.56 - 5.34: 68 5.34 - 7.11: 24 7.11 - 8.89: 5 Bond angle restraints: 10320 Sorted by residual: angle pdb=" C SER A 188 " pdb=" N LYS A 189 " pdb=" CA LYS A 189 " ideal model delta sigma weight residual 122.40 127.76 -5.36 1.45e+00 4.76e-01 1.36e+01 angle pdb=" N SER D 188 " pdb=" CA SER D 188 " pdb=" C SER D 188 " ideal model delta sigma weight residual 112.89 108.54 4.35 1.24e+00 6.50e-01 1.23e+01 angle pdb=" C ASN A 28 " pdb=" N ASN A 29 " pdb=" CA ASN A 29 " ideal model delta sigma weight residual 121.54 128.21 -6.67 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C ASN C 28 " pdb=" N ASN C 29 " pdb=" CA ASN C 29 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C ASN B 28 " pdb=" N ASN B 29 " pdb=" CA ASN B 29 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 ... (remaining 10315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.00: 4306 22.00 - 43.99: 161 43.99 - 65.99: 30 65.99 - 87.98: 27 87.98 - 109.98: 16 Dihedral angle restraints: 4540 sinusoidal: 1828 harmonic: 2712 Sorted by residual: 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 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.86e+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 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 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 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 4537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1010 0.077 - 0.154: 197 0.154 - 0.231: 0 0.231 - 0.308: 4 0.308 - 0.385: 5 Chirality restraints: 1216 Sorted by residual: chirality pdb=" CA SER A 188 " pdb=" N SER A 188 " pdb=" C SER A 188 " pdb=" CB SER A 188 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.39 2.00e-01 2.50e+01 3.71e+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 2.75 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C3 BMA b 1 " pdb=" C2 BMA b 1 " pdb=" C4 BMA b 1 " pdb=" O3 BMA b 1 " both_signs ideal model delta sigma weight residual False 2.41 2.75 -0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 1213 not shown) Planarity restraints: 1292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 93 " 0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO D 94 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 94 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 94 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 93 " 0.040 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO C 94 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 94 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 94 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 187 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C VAL D 187 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL D 187 " -0.013 2.00e-02 2.50e+03 pdb=" N SER D 188 " -0.012 2.00e-02 2.50e+03 ... (remaining 1289 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 44 2.44 - 3.06: 4297 3.06 - 3.67: 11504 3.67 - 4.29: 18798 4.29 - 4.90: 31927 Nonbonded interactions: 66570 Sorted by model distance: nonbonded pdb="MN MN B 302 " pdb=" O HOH B 402 " model vdw 1.827 2.320 nonbonded pdb="MN MN A 302 " pdb=" O HOH A 402 " model vdw 1.831 2.320 nonbonded pdb="MN MN C 302 " pdb=" O HOH C 401 " model vdw 1.835 2.320 nonbonded pdb="MN MN D 302 " pdb=" O HOH D 402 " model vdw 1.836 2.320 nonbonded pdb=" OD2 ASP B 140 " pdb="MN MN B 302 " model vdw 1.880 2.320 ... (remaining 66565 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 'C' selection = chain 'D' } 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.500 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 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 0.058 7556 Z= 0.316 Angle : 0.872 8.893 10344 Z= 0.462 Chirality : 0.060 0.385 1216 Planarity : 0.007 0.060 1292 Dihedral : 16.281 109.979 2788 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.97 % Allowed : 7.39 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % 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: -1.34 (0.24), residues: 916 helix: None (None), residues: 0 sheet: 0.23 (0.26), residues: 368 loop : -1.78 (0.21), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 49 TYR 0.012 0.002 TYR A 52 PHE 0.025 0.004 PHE A 68 TRP 0.007 0.002 TRP B 59 HIS 0.005 0.002 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00677 ( 7548) covalent geometry : angle 0.86505 (10320) hydrogen bonds : bond 0.22565 ( 322) hydrogen bonds : angle 9.07119 ( 1035) link_ALPHA1-2 : bond 0.00550 ( 4) link_ALPHA1-2 : angle 1.60834 ( 12) link_ALPHA1-3 : bond 0.00018 ( 4) link_ALPHA1-3 : angle 3.06315 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8479 (tttm) cc_final: 0.8258 (tttp) REVERT: A 190 ARG cc_start: 0.8254 (mtp180) cc_final: 0.8044 (mmt-90) REVERT: B 176 LYS cc_start: 0.8290 (mmtp) cc_final: 0.7902 (mtpt) REVERT: B 190 ARG cc_start: 0.7957 (mmt90) cc_final: 0.7740 (mmt-90) REVERT: D 111 ASN cc_start: 0.7273 (m110) cc_final: 0.6738 (p0) REVERT: D 190 ARG cc_start: 0.8252 (mmm160) cc_final: 0.7958 (mmt-90) REVERT: D 231 LYS cc_start: 0.8805 (pttm) cc_final: 0.8536 (pttt) REVERT: C 2 GLN cc_start: 0.6381 (OUTLIER) cc_final: 0.6140 (mm110) REVERT: C 37 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6772 (m-30) outliers start: 16 outliers final: 3 residues processed: 158 average time/residue: 0.6208 time to fit residues: 103.0413 Evaluate side-chains 140 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 231 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 28 ASN A 41 ASN A 73 ASN A 133 ASN A 151 ASN A 160 ASN A 173 GLN B 23 HIS D 73 ASN D 151 ASN D 160 ASN D 173 GLN C 23 HIS C 160 ASN C 173 GLN C 174 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.126574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105159 restraints weight = 7787.082| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.59 r_work: 0.3159 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7556 Z= 0.180 Angle : 0.609 6.256 10344 Z= 0.336 Chirality : 0.047 0.160 1216 Planarity : 0.005 0.053 1292 Dihedral : 13.482 73.348 1243 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.96 % Allowed : 9.73 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % 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: -0.68 (0.26), residues: 916 helix: None (None), residues: 0 sheet: 0.51 (0.27), residues: 348 loop : -1.12 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 49 TYR 0.011 0.001 TYR A 52 PHE 0.018 0.002 PHE A 68 TRP 0.005 0.001 TRP D 59 HIS 0.003 0.001 HIS D 181 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 7548) covalent geometry : angle 0.60455 (10320) hydrogen bonds : bond 0.05733 ( 322) hydrogen bonds : angle 5.88788 ( 1035) link_ALPHA1-2 : bond 0.00241 ( 4) link_ALPHA1-2 : angle 1.69148 ( 12) link_ALPHA1-3 : bond 0.00591 ( 4) link_ALPHA1-3 : angle 1.47554 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8455 (tttm) cc_final: 0.8214 (tttp) REVERT: A 49 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8599 (ptm160) REVERT: A 176 LYS cc_start: 0.8531 (mptp) cc_final: 0.7773 (mtpt) REVERT: A 190 ARG cc_start: 0.8270 (mtp180) cc_final: 0.7879 (mmt-90) REVERT: B 49 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8675 (ptm160) REVERT: B 176 LYS cc_start: 0.8554 (mmtp) cc_final: 0.7912 (mtpt) REVERT: B 190 ARG cc_start: 0.8177 (mmt90) cc_final: 0.7711 (mmt-90) REVERT: D 176 LYS cc_start: 0.8590 (mptp) cc_final: 0.7759 (mtpt) REVERT: D 190 ARG cc_start: 0.8347 (mmm160) cc_final: 0.7944 (mmt-90) REVERT: C 37 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6971 (m-30) REVERT: C 208 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7867 (t70) outliers start: 24 outliers final: 10 residues processed: 152 average time/residue: 0.6405 time to fit residues: 102.1246 Evaluate side-chains 146 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 208 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 69 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 75 optimal weight: 0.1980 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.3528 r_free = 0.3528 target = 0.127073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105895 restraints weight = 7832.364| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.58 r_work: 0.3177 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7556 Z= 0.159 Angle : 0.576 5.881 10344 Z= 0.313 Chirality : 0.047 0.156 1216 Planarity : 0.005 0.054 1292 Dihedral : 10.312 59.350 1239 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.45 % Allowed : 11.33 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % 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: -0.37 (0.27), residues: 916 helix: None (None), residues: 0 sheet: 0.56 (0.28), residues: 352 loop : -0.80 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 49 TYR 0.011 0.001 TYR A 52 PHE 0.017 0.002 PHE B 68 TRP 0.005 0.001 TRP B 59 HIS 0.003 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7548) covalent geometry : angle 0.57207 (10320) hydrogen bonds : bond 0.04706 ( 322) hydrogen bonds : angle 5.36808 ( 1035) link_ALPHA1-2 : bond 0.00348 ( 4) link_ALPHA1-2 : angle 1.67504 ( 12) link_ALPHA1-3 : bond 0.00880 ( 4) link_ALPHA1-3 : angle 1.33421 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.320 Fit side-chains REVERT: A 35 LYS cc_start: 0.8497 (tttm) cc_final: 0.8237 (tttp) REVERT: A 49 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8577 (ptm160) REVERT: A 176 LYS cc_start: 0.8520 (mptp) cc_final: 0.7772 (mtpt) REVERT: A 190 ARG cc_start: 0.8230 (mtp180) cc_final: 0.7862 (mmt-90) REVERT: B 2 GLN cc_start: 0.6835 (mt0) cc_final: 0.6147 (mm110) REVERT: B 49 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8627 (ptm160) REVERT: B 176 LYS cc_start: 0.8560 (mmtp) cc_final: 0.7907 (mtpt) REVERT: B 190 ARG cc_start: 0.8148 (mmt90) cc_final: 0.7685 (mmt-90) REVERT: D 111 ASN cc_start: 0.7545 (m-40) cc_final: 0.6694 (p0) REVERT: D 176 LYS cc_start: 0.8543 (mptp) cc_final: 0.7744 (mtpt) REVERT: D 190 ARG cc_start: 0.8273 (mmm160) cc_final: 0.7843 (mmt-90) REVERT: C 2 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.6217 (mm110) REVERT: C 208 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7829 (t70) outliers start: 28 outliers final: 15 residues processed: 152 average time/residue: 0.6644 time to fit residues: 105.8076 Evaluate side-chains 155 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 208 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 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 = 0.3537 r_free = 0.3537 target = 0.127817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.106615 restraints weight = 7856.512| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.58 r_work: 0.3183 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7556 Z= 0.146 Angle : 0.553 5.748 10344 Z= 0.301 Chirality : 0.046 0.149 1216 Planarity : 0.004 0.055 1292 Dihedral : 7.982 55.370 1237 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.20 % Allowed : 12.44 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % 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: -0.26 (0.27), residues: 916 helix: None (None), residues: 0 sheet: 0.55 (0.28), residues: 352 loop : -0.64 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 49 TYR 0.011 0.001 TYR B 52 PHE 0.016 0.002 PHE A 68 TRP 0.005 0.001 TRP B 246 HIS 0.003 0.001 HIS D 181 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7548) covalent geometry : angle 0.54856 (10320) hydrogen bonds : bond 0.04184 ( 322) hydrogen bonds : angle 5.18119 ( 1035) link_ALPHA1-2 : bond 0.00271 ( 4) link_ALPHA1-2 : angle 1.76356 ( 12) link_ALPHA1-3 : bond 0.00915 ( 4) link_ALPHA1-3 : angle 1.43158 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.290 Fit side-chains REVERT: A 35 LYS cc_start: 0.8500 (tttm) cc_final: 0.8242 (tttp) REVERT: A 49 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8532 (ptm160) REVERT: A 176 LYS cc_start: 0.8531 (mptp) cc_final: 0.7727 (mtpt) REVERT: A 190 ARG cc_start: 0.8232 (mtp180) cc_final: 0.7838 (mmt-90) REVERT: B 49 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8555 (ptm160) REVERT: B 176 LYS cc_start: 0.8551 (mmtp) cc_final: 0.7902 (mtpt) REVERT: B 190 ARG cc_start: 0.8168 (mmt90) cc_final: 0.7734 (mmt-90) REVERT: D 111 ASN cc_start: 0.7488 (m-40) cc_final: 0.6661 (p0) REVERT: D 176 LYS cc_start: 0.8536 (mptp) cc_final: 0.7738 (mtpt) REVERT: D 190 ARG cc_start: 0.8252 (mmm160) cc_final: 0.7806 (mmt-90) REVERT: C 2 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.6257 (mm110) REVERT: C 208 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7819 (t70) outliers start: 26 outliers final: 13 residues processed: 148 average time/residue: 0.6591 time to fit residues: 102.1450 Evaluate side-chains 150 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 208 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN D 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.126808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.105568 restraints weight = 7842.413| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.59 r_work: 0.3163 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7556 Z= 0.165 Angle : 0.563 6.148 10344 Z= 0.307 Chirality : 0.046 0.148 1216 Planarity : 0.004 0.055 1292 Dihedral : 7.590 53.052 1237 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.06 % Allowed : 12.81 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % 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: -0.20 (0.27), residues: 916 helix: None (None), residues: 0 sheet: 0.57 (0.28), residues: 352 loop : -0.59 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 163 TYR 0.012 0.001 TYR A 52 PHE 0.018 0.002 PHE B 68 TRP 0.005 0.001 TRP B 59 HIS 0.003 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7548) covalent geometry : angle 0.55764 (10320) hydrogen bonds : bond 0.04235 ( 322) hydrogen bonds : angle 5.20355 ( 1035) link_ALPHA1-2 : bond 0.00240 ( 4) link_ALPHA1-2 : angle 1.84472 ( 12) link_ALPHA1-3 : bond 0.00821 ( 4) link_ALPHA1-3 : angle 1.39895 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.175 Fit side-chains REVERT: A 35 LYS cc_start: 0.8509 (tttm) cc_final: 0.8248 (tttp) REVERT: A 49 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8562 (ptm160) REVERT: A 176 LYS cc_start: 0.8525 (mptp) cc_final: 0.7722 (mtpt) REVERT: A 190 ARG cc_start: 0.8225 (mtp180) cc_final: 0.7829 (mmt-90) REVERT: B 2 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6122 (mm110) REVERT: B 31 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8747 (tt) REVERT: B 49 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8581 (ptm160) REVERT: B 176 LYS cc_start: 0.8558 (mmtp) cc_final: 0.7899 (mtpt) REVERT: B 190 ARG cc_start: 0.8204 (mmt90) cc_final: 0.7670 (mmt-90) REVERT: D 176 LYS cc_start: 0.8535 (mptp) cc_final: 0.7737 (mtpt) REVERT: D 190 ARG cc_start: 0.8264 (mmm160) cc_final: 0.7794 (mmt-90) REVERT: C 2 GLN cc_start: 0.6631 (OUTLIER) cc_final: 0.6260 (mm110) REVERT: C 190 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7094 (mpt-90) outliers start: 33 outliers final: 16 residues processed: 153 average time/residue: 0.6590 time to fit residues: 105.5711 Evaluate side-chains 153 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain B residue 2 GLN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 206 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 60 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 0.1980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 234 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 = 0.3505 r_free = 0.3505 target = 0.125358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.104006 restraints weight = 7880.673| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.59 r_work: 0.3139 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7556 Z= 0.208 Angle : 0.596 6.665 10344 Z= 0.325 Chirality : 0.047 0.152 1216 Planarity : 0.005 0.055 1292 Dihedral : 7.761 52.500 1237 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.19 % Allowed : 12.68 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % 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: -0.16 (0.27), residues: 916 helix: None (None), residues: 0 sheet: 0.62 (0.28), residues: 352 loop : -0.58 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 49 TYR 0.015 0.001 TYR B 52 PHE 0.018 0.003 PHE A 68 TRP 0.004 0.001 TRP C 246 HIS 0.004 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 7548) covalent geometry : angle 0.59079 (10320) hydrogen bonds : bond 0.04538 ( 322) hydrogen bonds : angle 5.41112 ( 1035) link_ALPHA1-2 : bond 0.00148 ( 4) link_ALPHA1-2 : angle 2.00320 ( 12) link_ALPHA1-3 : bond 0.00671 ( 4) link_ALPHA1-3 : angle 1.49683 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8497 (tttm) cc_final: 0.8226 (tttp) REVERT: A 49 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8034 (ptm160) REVERT: A 176 LYS cc_start: 0.8516 (mptp) cc_final: 0.7716 (mtpt) REVERT: B 2 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.6189 (mm110) REVERT: B 49 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8059 (ptm160) REVERT: B 176 LYS cc_start: 0.8572 (mmtp) cc_final: 0.7894 (mtpt) REVERT: B 190 ARG cc_start: 0.8213 (mmt90) cc_final: 0.7683 (mmt-90) REVERT: D 176 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7721 (mtpt) REVERT: D 190 ARG cc_start: 0.8292 (mmm160) cc_final: 0.7820 (mmt-90) REVERT: C 2 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.6280 (mm110) REVERT: C 190 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7111 (mpt-90) outliers start: 34 outliers final: 15 residues processed: 148 average time/residue: 0.6668 time to fit residues: 103.2720 Evaluate side-chains 147 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain B residue 2 GLN Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 190 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 21 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 28 ASN D 28 ASN C 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.126074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.104868 restraints weight = 7886.870| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.59 r_work: 0.3156 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7556 Z= 0.174 Angle : 0.568 6.241 10344 Z= 0.311 Chirality : 0.046 0.149 1216 Planarity : 0.004 0.055 1292 Dihedral : 7.654 54.757 1237 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.19 % Allowed : 13.30 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % 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: -0.15 (0.27), residues: 916 helix: None (None), residues: 0 sheet: 0.60 (0.28), residues: 352 loop : -0.55 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 49 TYR 0.013 0.001 TYR A 52 PHE 0.017 0.003 PHE A 68 TRP 0.005 0.001 TRP B 59 HIS 0.003 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 7548) covalent geometry : angle 0.56310 (10320) hydrogen bonds : bond 0.04255 ( 322) hydrogen bonds : angle 5.25054 ( 1035) link_ALPHA1-2 : bond 0.00262 ( 4) link_ALPHA1-2 : angle 1.82457 ( 12) link_ALPHA1-3 : bond 0.00559 ( 4) link_ALPHA1-3 : angle 1.45635 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.276 Fit side-chains REVERT: A 35 LYS cc_start: 0.8479 (tttm) cc_final: 0.8207 (tttp) REVERT: A 49 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8555 (ptm160) REVERT: A 176 LYS cc_start: 0.8519 (mptp) cc_final: 0.7720 (mtpt) REVERT: A 208 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7750 (t70) REVERT: B 2 GLN cc_start: 0.6786 (OUTLIER) cc_final: 0.6148 (mm110) REVERT: B 49 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8588 (ptm160) REVERT: B 176 LYS cc_start: 0.8547 (mmtp) cc_final: 0.7883 (mtpt) REVERT: B 190 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7676 (mmt-90) REVERT: D 176 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7737 (mtpt) REVERT: D 190 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7774 (mmt-90) REVERT: C 2 GLN cc_start: 0.6578 (OUTLIER) cc_final: 0.6246 (mm110) REVERT: C 190 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7095 (mpt-90) outliers start: 34 outliers final: 14 residues processed: 142 average time/residue: 0.6856 time to fit residues: 101.8378 Evaluate side-chains 148 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain B residue 2 GLN Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 190 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 28 ASN B 234 ASN D 28 ASN C 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106899 restraints weight = 7935.582| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.59 r_work: 0.3185 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7556 Z= 0.129 Angle : 0.536 5.888 10344 Z= 0.293 Chirality : 0.044 0.146 1216 Planarity : 0.004 0.054 1292 Dihedral : 7.327 54.786 1237 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.08 % Allowed : 15.02 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % 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: -0.15 (0.27), residues: 916 helix: None (None), residues: 0 sheet: 0.56 (0.28), residues: 352 loop : -0.51 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.010 0.001 TYR D 52 PHE 0.016 0.002 PHE A 68 TRP 0.005 0.001 TRP B 246 HIS 0.002 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7548) covalent geometry : angle 0.53182 (10320) hydrogen bonds : bond 0.03874 ( 322) hydrogen bonds : angle 4.99770 ( 1035) link_ALPHA1-2 : bond 0.00408 ( 4) link_ALPHA1-2 : angle 1.66064 ( 12) link_ALPHA1-3 : bond 0.00561 ( 4) link_ALPHA1-3 : angle 1.44458 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.273 Fit side-chains REVERT: A 35 LYS cc_start: 0.8485 (tttm) cc_final: 0.8222 (tttp) REVERT: A 49 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8527 (ptm160) REVERT: A 176 LYS cc_start: 0.8515 (mptp) cc_final: 0.7723 (mtpt) REVERT: A 208 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7782 (t70) REVERT: B 2 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6120 (mm110) REVERT: B 49 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8552 (ptm160) REVERT: B 176 LYS cc_start: 0.8553 (mmtp) cc_final: 0.7898 (mtpt) REVERT: B 190 ARG cc_start: 0.8154 (mmt90) cc_final: 0.7633 (mmt-90) REVERT: D 176 LYS cc_start: 0.8537 (mptp) cc_final: 0.7742 (mtpt) REVERT: D 190 ARG cc_start: 0.8227 (mmm160) cc_final: 0.7799 (mmt-90) REVERT: C 2 GLN cc_start: 0.6495 (OUTLIER) cc_final: 0.6235 (mm110) REVERT: C 190 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7126 (mpt-90) outliers start: 25 outliers final: 12 residues processed: 142 average time/residue: 0.6658 time to fit residues: 99.0217 Evaluate side-chains 148 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain B residue 2 GLN Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 190 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 4 optimal weight: 0.0980 chunk 52 optimal weight: 0.4980 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN A 28 ASN B 28 ASN B 234 ASN D 28 ASN C 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103959 restraints weight = 7797.451| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.58 r_work: 0.3139 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7556 Z= 0.214 Angle : 0.599 6.757 10344 Z= 0.326 Chirality : 0.047 0.147 1216 Planarity : 0.005 0.056 1292 Dihedral : 7.758 59.722 1237 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 3.57 % Allowed : 14.66 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % 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: -0.11 (0.27), residues: 916 helix: None (None), residues: 0 sheet: 0.61 (0.28), residues: 352 loop : -0.51 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.014 0.001 TYR A 52 PHE 0.018 0.003 PHE A 68 TRP 0.004 0.001 TRP A 59 HIS 0.003 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 7548) covalent geometry : angle 0.59319 (10320) hydrogen bonds : bond 0.04446 ( 322) hydrogen bonds : angle 5.33069 ( 1035) link_ALPHA1-2 : bond 0.00152 ( 4) link_ALPHA1-2 : angle 1.99059 ( 12) link_ALPHA1-3 : bond 0.00425 ( 4) link_ALPHA1-3 : angle 1.55620 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.282 Fit side-chains REVERT: A 35 LYS cc_start: 0.8480 (tttm) cc_final: 0.8206 (tttp) REVERT: A 49 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8046 (ptm160) REVERT: A 176 LYS cc_start: 0.8507 (mptp) cc_final: 0.7718 (mtpt) REVERT: A 208 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7787 (t70) REVERT: B 2 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6193 (mm110) REVERT: B 49 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.7984 (ptm160) REVERT: B 176 LYS cc_start: 0.8558 (mmtp) cc_final: 0.7888 (mtpt) REVERT: B 190 ARG cc_start: 0.8221 (mmt90) cc_final: 0.7678 (mmt-90) REVERT: D 176 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7729 (mtpt) REVERT: D 190 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7838 (mmt-90) REVERT: C 2 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.6299 (mm110) REVERT: C 190 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7106 (mpt-90) outliers start: 29 outliers final: 14 residues processed: 137 average time/residue: 0.7009 time to fit residues: 100.3752 Evaluate side-chains 140 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain B residue 2 GLN Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 190 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 73 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN A 28 ASN B 28 ASN D 28 ASN C 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104918 restraints weight = 7870.128| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.58 r_work: 0.3152 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7556 Z= 0.176 Angle : 0.573 6.195 10344 Z= 0.312 Chirality : 0.046 0.149 1216 Planarity : 0.004 0.056 1292 Dihedral : 7.637 59.820 1237 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.08 % Allowed : 15.02 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % 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: -0.10 (0.27), residues: 916 helix: None (None), residues: 0 sheet: 0.63 (0.28), residues: 352 loop : -0.51 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.013 0.001 TYR A 52 PHE 0.017 0.003 PHE A 68 TRP 0.004 0.001 TRP B 218 HIS 0.003 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 7548) covalent geometry : angle 0.56811 (10320) hydrogen bonds : bond 0.04232 ( 322) hydrogen bonds : angle 5.20257 ( 1035) link_ALPHA1-2 : bond 0.00288 ( 4) link_ALPHA1-2 : angle 1.80126 ( 12) link_ALPHA1-3 : bond 0.00411 ( 4) link_ALPHA1-3 : angle 1.52379 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.288 Fit side-chains REVERT: A 35 LYS cc_start: 0.8482 (tttm) cc_final: 0.8209 (tttp) REVERT: A 49 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8559 (ptm160) REVERT: A 176 LYS cc_start: 0.8503 (mptp) cc_final: 0.7706 (mtpt) REVERT: A 208 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7799 (t70) REVERT: B 2 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6165 (mm110) REVERT: B 49 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8526 (ptm160) REVERT: B 176 LYS cc_start: 0.8544 (mmtp) cc_final: 0.7886 (mtpt) REVERT: B 190 ARG cc_start: 0.8207 (mmt90) cc_final: 0.7665 (mmt-90) REVERT: D 176 LYS cc_start: 0.8540 (mptp) cc_final: 0.7739 (mtpt) REVERT: D 190 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7816 (mmt-90) REVERT: C 2 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.6277 (mm110) REVERT: C 190 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7098 (mpt-90) outliers start: 25 outliers final: 14 residues processed: 134 average time/residue: 0.7021 time to fit residues: 98.3360 Evaluate side-chains 144 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain B residue 2 GLN Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 190 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 1 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN A 28 ASN B 28 ASN D 28 ASN C 28 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 = 0.3498 r_free = 0.3498 target = 0.124826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.103537 restraints weight = 7886.643| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.59 r_work: 0.3133 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7556 Z= 0.226 Angle : 0.614 6.850 10344 Z= 0.332 Chirality : 0.047 0.148 1216 Planarity : 0.005 0.057 1292 Dihedral : 7.564 56.505 1237 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.33 % Allowed : 15.27 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % 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: -0.09 (0.27), residues: 916 helix: None (None), residues: 0 sheet: 0.67 (0.28), residues: 352 loop : -0.53 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.015 0.001 TYR B 52 PHE 0.018 0.003 PHE A 68 TRP 0.004 0.001 TRP B 218 HIS 0.004 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 7548) covalent geometry : angle 0.60898 (10320) hydrogen bonds : bond 0.04544 ( 322) hydrogen bonds : angle 5.38239 ( 1035) link_ALPHA1-2 : bond 0.00152 ( 4) link_ALPHA1-2 : angle 1.98602 ( 12) link_ALPHA1-3 : bond 0.00329 ( 4) link_ALPHA1-3 : angle 1.61424 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2878.37 seconds wall clock time: 49 minutes 54.47 seconds (2994.47 seconds total)