Starting phenix.real_space_refine on Wed Jun 3 13:55:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21au_67539/06_2026/21au_67539.cif Found real_map, /net/cci-nas-00/data/ceres_data/21au_67539/06_2026/21au_67539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21au_67539/06_2026/21au_67539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21au_67539/06_2026/21au_67539.map" model { file = "/net/cci-nas-00/data/ceres_data/21au_67539/06_2026/21au_67539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21au_67539/06_2026/21au_67539.cif" } resolution = 2.69 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 3838 2.51 5 N 1026 2.21 5 O 1227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6135 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 982 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "B" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2424 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 296} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.40, per 1000 atoms: 0.23 Number of scatterers: 6135 At special positions: 0 Unit cell: (60.8, 118.75, 110.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1227 8.00 N 1026 7.00 C 3838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 80 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 103 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 49 " distance=2.03 Simple disulfide: pdb=" SG CYS H 143 " - pdb=" SG CYS H 156 " distance=2.04 Simple disulfide: pdb=" SG CYS H 180 " - pdb=" SG CYS H 327 " distance=2.03 Simple disulfide: pdb=" SG CYS H 206 " - pdb=" SG CYS H 216 " distance=2.03 Simple disulfide: pdb=" SG CYS H 258 " - pdb=" SG CYS H 266 " distance=2.06 Simple disulfide: pdb=" SG CYS H 258 " - pdb=" SG CYS H 305 " distance=2.05 Simple disulfide: pdb=" SG CYS H 266 " - pdb=" SG CYS H 303 " distance=2.05 Simple disulfide: pdb=" SG CYS H 274 " - pdb=" SG CYS H 280 " distance=2.03 Simple disulfide: pdb=" SG CYS H 287 " - pdb=" SG CYS H 292 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG E 1 " - " ASN D 25 " " NAG F 1 " - " ASN H 63 " " NAG G 1 " - " ASN H 33 " Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 275.3 milliseconds 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1390 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 19 sheets defined 14.3% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.573A pdb=" N ILE A 31 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.069A pdb=" N LEU B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.728A pdb=" N THR C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.586A pdb=" N ASP D 83 " --> pdb=" O GLN D 80 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU D 84 " --> pdb=" O THR D 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 80 through 84' Processing helix chain 'H' and resid 43 through 53 Processing helix chain 'H' and resid 54 through 65 Processing helix chain 'H' and resid 76 through 80 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.777A pdb=" N ARG H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP H 92 " --> pdb=" O TYR H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 88 through 92' Processing helix chain 'H' and resid 97 through 104 Processing helix chain 'H' and resid 160 through 163 removed outlier: 3.629A pdb=" N SER H 163 " --> pdb=" O SER H 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 160 through 163' Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 187 through 202 Processing helix chain 'H' and resid 252 through 254 No H-bonds generated for 'chain 'H' and resid 252 through 254' Processing helix chain 'H' and resid 267 through 278 removed outlier: 4.074A pdb=" N GLY H 278 " --> pdb=" O CYS H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.809A pdb=" N TRP A 33 " --> pdb=" O HIS A 99 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A 34 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.752A pdb=" N CYS A 96 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRP A 115 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG A 98 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.610A pdb=" N SER B 7 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 67 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.757A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP B 35 " --> pdb=" O MET B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.564A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.669A pdb=" N GLY C 10 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TRP C 33 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET C 34 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.669A pdb=" N GLY C 10 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N CYS C 96 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP C 115 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG C 98 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C 111 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.289A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.289A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.579A pdb=" N SER D 71 " --> pdb=" O SER D 68 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 70 through 71 removed outlier: 6.682A pdb=" N TYR H 70 " --> pdb=" O LEU H 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'H' and resid 81 through 83 removed outlier: 6.568A pdb=" N SER H 81 " --> pdb=" O TRP H 174 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE H 129 " --> pdb=" O LEU H 173 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE H 175 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU H 131 " --> pdb=" O ILE H 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 147 through 149 Processing sheet with id=AB7, first strand: chain 'H' and resid 177 through 180 removed outlier: 3.840A pdb=" N LYS H 207 " --> pdb=" O THR H 336 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 177 through 180 removed outlier: 4.186A pdb=" N ALA H 228 " --> pdb=" O MET H 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 244 through 248 Processing sheet with id=AC1, first strand: chain 'H' and resid 256 through 257 234 hydrogen bonds defined for protein. 573 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: 0.98 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1969 1.35 - 1.48: 1695 1.48 - 1.61: 2558 1.61 - 1.73: 0 1.73 - 1.86: 59 Bond restraints: 6281 Sorted by residual: bond pdb=" CA CYS H 258 " pdb=" CB CYS H 258 " ideal model delta sigma weight residual 1.527 1.502 0.026 1.49e-02 4.50e+03 2.94e+00 bond pdb=" CB CYS H 305 " pdb=" SG CYS H 305 " ideal model delta sigma weight residual 1.808 1.863 -0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" C5 MAN F 7 " pdb=" O5 MAN F 7 " ideal model delta sigma weight residual 1.418 1.451 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C1 MAN F 7 " pdb=" C2 MAN F 7 " ideal model delta sigma weight residual 1.526 1.558 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 ... (remaining 6276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 8374 2.54 - 5.08: 128 5.08 - 7.61: 9 7.61 - 10.15: 1 10.15 - 12.69: 2 Bond angle restraints: 8514 Sorted by residual: angle pdb=" CA CYS H 266 " pdb=" CB CYS H 266 " pdb=" SG CYS H 266 " ideal model delta sigma weight residual 114.40 127.09 -12.69 2.30e+00 1.89e-01 3.04e+01 angle pdb=" CA CYS H 258 " pdb=" CB CYS H 258 " pdb=" SG CYS H 258 " ideal model delta sigma weight residual 114.40 126.99 -12.59 2.30e+00 1.89e-01 3.00e+01 angle pdb=" C ASN B 30 " pdb=" CA ASN B 30 " pdb=" CB ASN B 30 " ideal model delta sigma weight residual 117.23 111.00 6.23 1.36e+00 5.41e-01 2.10e+01 angle pdb=" N TYR A 110 " pdb=" CA TYR A 110 " pdb=" C TYR A 110 " ideal model delta sigma weight residual 110.91 115.14 -4.23 1.17e+00 7.31e-01 1.31e+01 angle pdb=" N VAL H 128 " pdb=" CA VAL H 128 " pdb=" C VAL H 128 " ideal model delta sigma weight residual 111.81 108.70 3.11 8.60e-01 1.35e+00 1.31e+01 ... (remaining 8509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 3666 21.50 - 43.00: 160 43.00 - 64.49: 25 64.49 - 85.99: 14 85.99 - 107.49: 4 Dihedral angle restraints: 3869 sinusoidal: 1670 harmonic: 2199 Sorted by residual: dihedral pdb=" CB CYS H 258 " pdb=" SG CYS H 258 " pdb=" SG CYS H 266 " pdb=" CB CYS H 266 " ideal model delta sinusoidal sigma weight residual -86.00 -28.94 -57.06 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CB CYS H 26 " pdb=" SG CYS H 26 " pdb=" SG CYS H 49 " pdb=" CB CYS H 49 " ideal model delta sinusoidal sigma weight residual -86.00 -125.39 39.39 1 1.00e+01 1.00e-02 2.18e+01 dihedral pdb=" CA CYS H 258 " pdb=" C CYS H 258 " pdb=" N TYR H 259 " pdb=" CA TYR H 259 " ideal model delta harmonic sigma weight residual 180.00 159.92 20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 3866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 758 0.053 - 0.107: 140 0.107 - 0.160: 35 0.160 - 0.213: 1 0.213 - 0.267: 1 Chirality restraints: 935 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE A 34 " pdb=" CA ILE A 34 " pdb=" CG1 ILE A 34 " pdb=" CG2 ILE A 34 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CB ILE H 25 " pdb=" CA ILE H 25 " pdb=" CG1 ILE H 25 " pdb=" CG2 ILE H 25 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 932 not shown) Planarity restraints: 1091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 121 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO H 122 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO H 122 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 122 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 7 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO D 8 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 8 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 8 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 181 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO H 182 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 182 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 182 " 0.019 5.00e-02 4.00e+02 ... (remaining 1088 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 940 2.77 - 3.30: 5180 3.30 - 3.84: 9909 3.84 - 4.37: 12354 4.37 - 4.90: 21092 Nonbonded interactions: 49475 Sorted by model distance: nonbonded pdb=" OG SER H 198 " pdb=" O ILE H 239 " model vdw 2.241 3.040 nonbonded pdb=" NH1 ARG A 59 " pdb=" OH TYR A 110 " model vdw 2.271 3.120 nonbonded pdb=" OD1 ASN D 28 " pdb=" N MET D 29 " model vdw 2.296 3.120 nonbonded pdb=" NE2 GLN H 199 " pdb=" O PHE H 213 " model vdw 2.337 3.120 nonbonded pdb=" O GLY C 106 " pdb=" NE1 TRP D 92 " model vdw 2.346 3.120 ... (remaining 49470 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' } 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: 4.300 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.890 Find NCS groups from input model: 0.040 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 0.004 0.055 6307 Z= 0.180 Angle : 0.781 12.775 8577 Z= 0.421 Chirality : 0.046 0.267 935 Planarity : 0.005 0.054 1088 Dihedral : 13.043 107.492 2434 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % 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: -0.34 (0.30), residues: 770 helix: 1.24 (0.70), residues: 65 sheet: 0.58 (0.33), residues: 251 loop : -0.94 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 281 TYR 0.014 0.002 TYR H 259 PHE 0.014 0.001 PHE H 130 TRP 0.008 0.001 TRP H 141 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 ( 6281) covalent geometry : angle 0.74252 / 0.41 ( 8514) SS BOND : bond 0.00940 / 0.82 ( 15) SS BOND : angle 3.75844 / 2.60 ( 30) hydrogen bonds : bond 0.21491 / 14.05 ( 212) hydrogen bonds : angle 7.99025 / 5.61 ( 573) link_ALPHA1-3 : bond 0.00307 / 0.16 ( 2) link_ALPHA1-3 : angle 2.24748 / 1.15 ( 6) link_ALPHA1-6 : bond 0.00351 / 0.18 ( 2) link_ALPHA1-6 : angle 1.72467 / 0.87 ( 6) link_BETA1-4 : bond 0.00272 / 0.14 ( 4) link_BETA1-4 : angle 2.08901 / 1.10 ( 12) link_NAG-ASN : bond 0.00173 / 0.09 ( 3) link_NAG-ASN : angle 1.26094 / 0.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: C 85 ASN cc_start: 0.7977 (t0) cc_final: 0.7476 (t0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.7144 time to fit residues: 84.4045 Evaluate side-chains 100 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0070 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.0170 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 3 GLN B 100 GLN C 77 ASN D 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.143959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.122883 restraints weight = 6370.977| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.54 r_work: 0.3236 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6307 Z= 0.121 Angle : 0.649 12.157 8577 Z= 0.332 Chirality : 0.045 0.186 935 Planarity : 0.005 0.051 1088 Dihedral : 8.213 76.447 1067 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.25 % Favored : 96.62 % Rotamer: Outliers : 1.98 % Allowed : 8.52 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % 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 (0.31), residues: 770 helix: 1.15 (0.68), residues: 66 sheet: 0.68 (0.33), residues: 276 loop : -0.71 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 281 TYR 0.012 0.002 TYR C 95 PHE 0.015 0.001 PHE H 130 TRP 0.012 0.001 TRP H 141 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 6281) covalent geometry : angle 0.61641 / 0.32 ( 8514) SS BOND : bond 0.00899 / 0.77 ( 15) SS BOND : angle 2.97808 / 2.25 ( 30) hydrogen bonds : bond 0.04411 / 3.01 ( 212) hydrogen bonds : angle 5.82449 / 4.12 ( 573) link_ALPHA1-3 : bond 0.00729 / 0.38 ( 2) link_ALPHA1-3 : angle 1.94997 / 1.02 ( 6) link_ALPHA1-6 : bond 0.00438 / 0.23 ( 2) link_ALPHA1-6 : angle 1.57210 / 0.82 ( 6) link_BETA1-4 : bond 0.00320 / 0.16 ( 4) link_BETA1-4 : angle 2.06346 / 1.06 ( 12) link_NAG-ASN : bond 0.00156 / 0.08 ( 3) link_NAG-ASN : angle 1.46359 / 0.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: B 24 ARG cc_start: 0.7975 (ttp-110) cc_final: 0.7737 (tmm160) REVERT: C 85 ASN cc_start: 0.8173 (t0) cc_final: 0.7486 (t0) REVERT: H 193 GLU cc_start: 0.7220 (tt0) cc_final: 0.6660 (tm-30) REVERT: H 240 MET cc_start: 0.9294 (ptt) cc_final: 0.9056 (ptt) REVERT: H 288 LYS cc_start: 0.7278 (tppt) cc_final: 0.6765 (tttp) outliers start: 13 outliers final: 4 residues processed: 108 average time/residue: 0.7296 time to fit residues: 81.6425 Evaluate side-chains 103 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 284 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 82 GLN B 3 GLN B 30 ASN C 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.141204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.120027 restraints weight = 6315.106| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.54 r_work: 0.3197 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6307 Z= 0.160 Angle : 0.685 12.132 8577 Z= 0.350 Chirality : 0.047 0.207 935 Planarity : 0.005 0.053 1088 Dihedral : 8.080 73.946 1067 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 2.44 % Allowed : 9.74 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % 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 (0.30), residues: 770 helix: 1.21 (0.67), residues: 66 sheet: 0.67 (0.33), residues: 274 loop : -0.77 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 91 TYR 0.014 0.002 TYR C 95 PHE 0.016 0.002 PHE H 130 TRP 0.013 0.002 TRP H 141 HIS 0.006 0.002 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 6281) covalent geometry : angle 0.65367 / 0.34 ( 8514) SS BOND : bond 0.01068 / 0.89 ( 15) SS BOND : angle 3.02940 / 2.29 ( 30) hydrogen bonds : bond 0.04362 / 2.94 ( 212) hydrogen bonds : angle 5.44099 / 3.84 ( 573) link_ALPHA1-3 : bond 0.00639 / 0.34 ( 2) link_ALPHA1-3 : angle 1.95434 / 0.99 ( 6) link_ALPHA1-6 : bond 0.00339 / 0.18 ( 2) link_ALPHA1-6 : angle 1.54518 / 0.81 ( 6) link_BETA1-4 : bond 0.00340 / 0.17 ( 4) link_BETA1-4 : angle 2.15373 / 1.12 ( 12) link_NAG-ASN : bond 0.00163 / 0.08 ( 3) link_NAG-ASN : angle 1.46900 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: C 83 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8397 (mtm) REVERT: C 85 ASN cc_start: 0.8133 (t0) cc_final: 0.7449 (t0) REVERT: C 90 ASP cc_start: 0.8870 (m-30) cc_final: 0.8647 (m-30) REVERT: H 125 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8681 (tttm) REVERT: H 151 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7056 (tp30) REVERT: H 170 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7984 (p0) REVERT: H 288 LYS cc_start: 0.7260 (tppt) cc_final: 0.6761 (tttp) outliers start: 16 outliers final: 5 residues processed: 105 average time/residue: 0.6900 time to fit residues: 75.1940 Evaluate side-chains 108 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 266 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 82 GLN B 3 GLN C 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.128580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.106292 restraints weight = 6221.248| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.51 r_work: 0.2959 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6307 Z= 0.139 Angle : 0.657 12.116 8577 Z= 0.335 Chirality : 0.046 0.192 935 Planarity : 0.005 0.052 1088 Dihedral : 7.850 71.417 1067 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer: Outliers : 2.44 % Allowed : 11.72 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % 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 (0.31), residues: 770 helix: 1.44 (0.67), residues: 66 sheet: 0.72 (0.33), residues: 273 loop : -0.75 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 91 TYR 0.014 0.002 TYR C 95 PHE 0.016 0.001 PHE H 130 TRP 0.013 0.002 TRP H 141 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6281) covalent geometry : angle 0.62702 / 0.32 ( 8514) SS BOND : bond 0.00967 / 0.80 ( 15) SS BOND : angle 2.89137 / 2.23 ( 30) hydrogen bonds : bond 0.03949 / 2.67 ( 212) hydrogen bonds : angle 5.25010 / 3.72 ( 573) link_ALPHA1-3 : bond 0.00657 / 0.35 ( 2) link_ALPHA1-3 : angle 1.87346 / 0.95 ( 6) link_ALPHA1-6 : bond 0.00340 / 0.18 ( 2) link_ALPHA1-6 : angle 1.56217 / 0.81 ( 6) link_BETA1-4 : bond 0.00367 / 0.18 ( 4) link_BETA1-4 : angle 2.09826 / 1.09 ( 12) link_NAG-ASN : bond 0.00173 / 0.09 ( 3) link_NAG-ASN : angle 1.46758 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8279 (m-30) cc_final: 0.7981 (m-30) REVERT: C 83 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8272 (mtm) REVERT: C 85 ASN cc_start: 0.8206 (t0) cc_final: 0.7409 (t0) REVERT: H 125 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8688 (tttm) REVERT: H 170 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8047 (p0) REVERT: H 261 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: H 288 LYS cc_start: 0.7101 (tppt) cc_final: 0.6609 (tttp) outliers start: 16 outliers final: 5 residues processed: 106 average time/residue: 0.7167 time to fit residues: 78.6871 Evaluate side-chains 106 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 266 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 3 GLN C 77 ASN D 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.125403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.102893 restraints weight = 6415.893| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.53 r_work: 0.2905 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6307 Z= 0.215 Angle : 0.766 13.757 8577 Z= 0.390 Chirality : 0.049 0.228 935 Planarity : 0.006 0.053 1088 Dihedral : 8.276 74.536 1067 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.97 % Rotamer: Outliers : 2.89 % Allowed : 12.33 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % 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: -0.17 (0.30), residues: 770 helix: 1.30 (0.66), residues: 66 sheet: 0.71 (0.33), residues: 271 loop : -0.90 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 91 TYR 0.016 0.003 TYR H 83 PHE 0.017 0.002 PHE H 130 TRP 0.015 0.002 TRP H 141 HIS 0.008 0.002 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.21 ( 6281) covalent geometry : angle 0.73183 / 0.38 ( 8514) SS BOND : bond 0.01398 / 1.15 ( 15) SS BOND : angle 3.34511 / 2.50 ( 30) hydrogen bonds : bond 0.04657 / 3.13 ( 212) hydrogen bonds : angle 5.35566 / 3.78 ( 573) link_ALPHA1-3 : bond 0.00387 / 0.20 ( 2) link_ALPHA1-3 : angle 2.14921 / 1.08 ( 6) link_ALPHA1-6 : bond 0.00317 / 0.17 ( 2) link_ALPHA1-6 : angle 1.53311 / 0.81 ( 6) link_BETA1-4 : bond 0.00372 / 0.18 ( 4) link_BETA1-4 : angle 2.41796 / 1.26 ( 12) link_NAG-ASN : bond 0.00192 / 0.10 ( 3) link_NAG-ASN : angle 1.63420 / 0.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8328 (m-30) cc_final: 0.8024 (m-30) REVERT: C 83 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8137 (mtm) REVERT: C 85 ASN cc_start: 0.8200 (t0) cc_final: 0.7463 (t0) REVERT: H 125 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8666 (tttm) REVERT: H 151 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7294 (tp30) REVERT: H 170 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8017 (p0) REVERT: H 288 LYS cc_start: 0.7194 (tppt) cc_final: 0.6658 (tttp) outliers start: 19 outliers final: 8 residues processed: 100 average time/residue: 0.6852 time to fit residues: 71.0336 Evaluate side-chains 104 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 266 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 72 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 0.0770 chunk 74 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 3 GLN C 77 ASN D 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.126434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.104106 restraints weight = 6328.884| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.51 r_work: 0.2976 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6307 Z= 0.170 Angle : 0.706 13.008 8577 Z= 0.360 Chirality : 0.047 0.193 935 Planarity : 0.005 0.053 1088 Dihedral : 8.050 72.766 1067 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.97 % Rotamer: Outliers : 2.74 % Allowed : 12.79 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % 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 (0.30), residues: 770 helix: 1.42 (0.67), residues: 66 sheet: 0.65 (0.33), residues: 273 loop : -0.85 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 91 TYR 0.015 0.002 TYR H 83 PHE 0.017 0.002 PHE H 130 TRP 0.014 0.002 TRP A 47 HIS 0.006 0.002 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 6281) covalent geometry : angle 0.67326 / 0.35 ( 8514) SS BOND : bond 0.01142 / 0.94 ( 15) SS BOND : angle 3.09968 / 2.37 ( 30) hydrogen bonds : bond 0.04213 / 2.85 ( 212) hydrogen bonds : angle 5.22247 / 3.70 ( 573) link_ALPHA1-3 : bond 0.00517 / 0.27 ( 2) link_ALPHA1-3 : angle 1.95073 / 0.99 ( 6) link_ALPHA1-6 : bond 0.00331 / 0.17 ( 2) link_ALPHA1-6 : angle 1.55362 / 0.81 ( 6) link_BETA1-4 : bond 0.00369 / 0.18 ( 4) link_BETA1-4 : angle 2.28805 / 1.19 ( 12) link_NAG-ASN : bond 0.00199 / 0.10 ( 3) link_NAG-ASN : angle 1.59601 / 0.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8286 (m-30) cc_final: 0.7982 (m-30) REVERT: A 100 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7776 (mm-30) REVERT: C 83 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8142 (mtm) REVERT: C 85 ASN cc_start: 0.8207 (t0) cc_final: 0.7472 (t0) REVERT: D 84 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8403 (mt-10) REVERT: H 125 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8649 (tttm) REVERT: H 170 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7984 (p0) REVERT: H 288 LYS cc_start: 0.7232 (tppt) cc_final: 0.6742 (tttp) outliers start: 18 outliers final: 8 residues processed: 102 average time/residue: 0.6915 time to fit residues: 73.1318 Evaluate side-chains 104 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 266 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 3 GLN B 53 HIS C 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.128517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.106334 restraints weight = 6266.607| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.50 r_work: 0.2963 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6307 Z= 0.121 Angle : 0.652 17.667 8577 Z= 0.331 Chirality : 0.045 0.289 935 Planarity : 0.005 0.053 1088 Dihedral : 7.641 68.927 1067 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.51 % Favored : 96.36 % Rotamer: Outliers : 2.44 % Allowed : 14.00 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % 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 (0.31), residues: 770 helix: 1.66 (0.68), residues: 66 sheet: 0.68 (0.33), residues: 276 loop : -0.73 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 91 TYR 0.013 0.002 TYR C 95 PHE 0.016 0.001 PHE H 130 TRP 0.013 0.001 TRP A 47 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 6281) covalent geometry : angle 0.62237 / 0.32 ( 8514) SS BOND : bond 0.01251 / 1.06 ( 15) SS BOND : angle 2.84414 / 2.23 ( 30) hydrogen bonds : bond 0.03644 / 2.48 ( 212) hydrogen bonds : angle 5.08874 / 3.62 ( 573) link_ALPHA1-3 : bond 0.00674 / 0.35 ( 2) link_ALPHA1-3 : angle 1.74705 / 0.89 ( 6) link_ALPHA1-6 : bond 0.00370 / 0.19 ( 2) link_ALPHA1-6 : angle 1.56578 / 0.80 ( 6) link_BETA1-4 : bond 0.00375 / 0.19 ( 4) link_BETA1-4 : angle 2.08600 / 1.09 ( 12) link_NAG-ASN : bond 0.00167 / 0.08 ( 3) link_NAG-ASN : angle 1.49217 / 0.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8238 (m-30) cc_final: 0.7932 (m-30) REVERT: A 100 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: C 19 ARG cc_start: 0.7653 (ttt180) cc_final: 0.7245 (tpt-90) REVERT: C 83 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8083 (mtm) REVERT: C 85 ASN cc_start: 0.8209 (t0) cc_final: 0.7555 (t0) REVERT: H 125 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8682 (tttm) REVERT: H 170 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8025 (p0) REVERT: H 288 LYS cc_start: 0.7192 (tppt) cc_final: 0.6701 (tttp) outliers start: 16 outliers final: 9 residues processed: 106 average time/residue: 0.6140 time to fit residues: 67.7750 Evaluate side-chains 109 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 284 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 0.0170 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 3 GLN C 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.128145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.105899 restraints weight = 6312.594| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.51 r_work: 0.2957 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6307 Z= 0.136 Angle : 0.680 18.692 8577 Z= 0.343 Chirality : 0.047 0.349 935 Planarity : 0.005 0.053 1088 Dihedral : 7.596 68.244 1067 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer: Outliers : 2.44 % Allowed : 14.46 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % 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 (0.31), residues: 770 helix: 1.72 (0.68), residues: 66 sheet: 0.70 (0.33), residues: 276 loop : -0.71 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 91 TYR 0.014 0.002 TYR C 95 PHE 0.016 0.001 PHE H 130 TRP 0.013 0.002 TRP H 141 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 6281) covalent geometry : angle 0.64935 / 0.33 ( 8514) SS BOND : bond 0.01439 / 1.22 ( 15) SS BOND : angle 2.99667 / 2.31 ( 30) hydrogen bonds : bond 0.03742 / 2.53 ( 212) hydrogen bonds : angle 5.02774 / 3.58 ( 573) link_ALPHA1-3 : bond 0.00591 / 0.31 ( 2) link_ALPHA1-3 : angle 1.83564 / 0.93 ( 6) link_ALPHA1-6 : bond 0.00334 / 0.17 ( 2) link_ALPHA1-6 : angle 1.56704 / 0.81 ( 6) link_BETA1-4 : bond 0.00372 / 0.19 ( 4) link_BETA1-4 : angle 2.08024 / 1.08 ( 12) link_NAG-ASN : bond 0.00164 / 0.08 ( 3) link_NAG-ASN : angle 1.45843 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8227 (m-30) cc_final: 0.7923 (m-30) REVERT: C 83 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8094 (mtm) REVERT: C 85 ASN cc_start: 0.8210 (t0) cc_final: 0.7567 (t0) REVERT: H 125 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8671 (tttm) REVERT: H 170 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8041 (p0) REVERT: H 288 LYS cc_start: 0.7238 (tppt) cc_final: 0.6740 (tttp) outliers start: 16 outliers final: 10 residues processed: 98 average time/residue: 0.6466 time to fit residues: 65.8554 Evaluate side-chains 105 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 284 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 3 GLN C 77 ASN D 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.117998 restraints weight = 6382.673| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.54 r_work: 0.3136 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6307 Z= 0.206 Angle : 0.803 20.155 8577 Z= 0.405 Chirality : 0.051 0.406 935 Planarity : 0.006 0.053 1088 Dihedral : 8.080 72.321 1067 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.44 % Allowed : 14.00 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % 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 (0.30), residues: 770 helix: 1.47 (0.67), residues: 66 sheet: 0.85 (0.33), residues: 261 loop : -0.84 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 304 TYR 0.016 0.003 TYR C 95 PHE 0.017 0.002 PHE H 130 TRP 0.014 0.002 TRP H 141 HIS 0.007 0.002 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 ( 6281) covalent geometry : angle 0.76996 / 0.39 ( 8514) SS BOND : bond 0.01743 / 1.46 ( 15) SS BOND : angle 3.43559 / 2.66 ( 30) hydrogen bonds : bond 0.04451 / 3.00 ( 212) hydrogen bonds : angle 5.18764 / 3.68 ( 573) link_ALPHA1-3 : bond 0.00369 / 0.19 ( 2) link_ALPHA1-3 : angle 2.07223 / 1.04 ( 6) link_ALPHA1-6 : bond 0.00342 / 0.18 ( 2) link_ALPHA1-6 : angle 1.55068 / 0.82 ( 6) link_BETA1-4 : bond 0.00393 / 0.20 ( 4) link_BETA1-4 : angle 2.35503 / 1.23 ( 12) link_NAG-ASN : bond 0.00185 / 0.09 ( 3) link_NAG-ASN : angle 1.60615 / 0.77 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8284 (m-30) cc_final: 0.8038 (m-30) REVERT: C 19 ARG cc_start: 0.7875 (ttt180) cc_final: 0.7397 (tpt-90) REVERT: C 83 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8239 (mtm) REVERT: C 85 ASN cc_start: 0.8175 (t0) cc_final: 0.7573 (t0) REVERT: H 170 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7923 (p0) REVERT: H 288 LYS cc_start: 0.7373 (tppt) cc_final: 0.6873 (tttp) outliers start: 16 outliers final: 9 residues processed: 96 average time/residue: 0.7091 time to fit residues: 70.6308 Evaluate side-chains 102 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 266 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 3 GLN C 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.141545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.120360 restraints weight = 6373.514| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.54 r_work: 0.3229 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6307 Z= 0.137 Angle : 0.711 19.116 8577 Z= 0.357 Chirality : 0.047 0.362 935 Planarity : 0.005 0.053 1088 Dihedral : 7.682 68.819 1067 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.98 % Allowed : 14.61 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % 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 (0.31), residues: 770 helix: 1.67 (0.67), residues: 66 sheet: 0.88 (0.34), residues: 263 loop : -0.72 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 304 TYR 0.013 0.002 TYR C 95 PHE 0.016 0.001 PHE H 130 TRP 0.013 0.002 TRP A 47 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 6281) covalent geometry : angle 0.67857 / 0.34 ( 8514) SS BOND : bond 0.01434 / 1.22 ( 15) SS BOND : angle 3.16363 / 2.45 ( 30) hydrogen bonds : bond 0.03772 / 2.56 ( 212) hydrogen bonds : angle 5.07120 / 3.61 ( 573) link_ALPHA1-3 : bond 0.00600 / 0.32 ( 2) link_ALPHA1-3 : angle 1.80054 / 0.92 ( 6) link_ALPHA1-6 : bond 0.00358 / 0.19 ( 2) link_ALPHA1-6 : angle 1.57288 / 0.81 ( 6) link_BETA1-4 : bond 0.00380 / 0.19 ( 4) link_BETA1-4 : angle 2.13697 / 1.12 ( 12) link_NAG-ASN : bond 0.00166 / 0.08 ( 3) link_NAG-ASN : angle 1.52667 / 0.76 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8231 (m-30) cc_final: 0.7974 (m-30) REVERT: C 19 ARG cc_start: 0.7829 (ttt180) cc_final: 0.7574 (tpt-90) REVERT: C 83 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8231 (mtm) REVERT: C 85 ASN cc_start: 0.8188 (t0) cc_final: 0.7560 (t0) REVERT: H 170 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7963 (p0) REVERT: H 288 LYS cc_start: 0.7254 (tppt) cc_final: 0.6753 (tttp) outliers start: 13 outliers final: 8 residues processed: 97 average time/residue: 0.7193 time to fit residues: 72.5038 Evaluate side-chains 103 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 266 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 29 optimal weight: 0.0670 chunk 40 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 3 GLN C 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.122371 restraints weight = 6373.893| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.53 r_work: 0.3259 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6307 Z= 0.117 Angle : 0.666 18.184 8577 Z= 0.333 Chirality : 0.046 0.335 935 Planarity : 0.005 0.052 1088 Dihedral : 7.269 64.489 1067 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.67 % Allowed : 14.92 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % 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: 0.24 (0.31), residues: 770 helix: 1.85 (0.68), residues: 66 sheet: 0.97 (0.34), residues: 263 loop : -0.62 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 304 TYR 0.012 0.001 TYR H 83 PHE 0.015 0.001 PHE H 130 TRP 0.013 0.001 TRP A 47 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 ( 6281) covalent geometry : angle 0.63556 / 0.32 ( 8514) SS BOND : bond 0.01192 / 1.01 ( 15) SS BOND : angle 2.95730 / 2.25 ( 30) hydrogen bonds : bond 0.03451 / 2.35 ( 212) hydrogen bonds : angle 4.94037 / 3.53 ( 573) link_ALPHA1-3 : bond 0.00634 / 0.33 ( 2) link_ALPHA1-3 : angle 1.74573 / 0.89 ( 6) link_ALPHA1-6 : bond 0.00347 / 0.18 ( 2) link_ALPHA1-6 : angle 1.56451 / 0.80 ( 6) link_BETA1-4 : bond 0.00369 / 0.19 ( 4) link_BETA1-4 : angle 2.00547 / 1.04 ( 12) link_NAG-ASN : bond 0.00139 / 0.07 ( 3) link_NAG-ASN : angle 1.41523 / 0.72 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.50 seconds wall clock time: 43 minutes 30.81 seconds (2610.81 seconds total)