Starting phenix.real_space_refine on Thu Jul 2 03:18:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gmt_34153/07_2026/8gmt_34153.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmt_34153/07_2026/8gmt_34153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gmt_34153/07_2026/8gmt_34153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmt_34153/07_2026/8gmt_34153.map" model { file = "/net/cci-nas-00/data/ceres_data/8gmt_34153/07_2026/8gmt_34153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmt_34153/07_2026/8gmt_34153.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gmt_34153/07_2026/8gmt_34153.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gmt_34153/07_2026/8gmt_34153.cif" } resolution = 3.31 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 2 5.21 5 S 29 5.16 5 C 3854 2.51 5 N 1045 2.21 5 O 1230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6172 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 250 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 28} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 722 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "F" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2508 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "G" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2508 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.58, per 1000 atoms: 0.26 Number of scatterers: 6172 At special positions: 0 Unit cell: (99.96, 95.2, 105.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 P 12 15.00 Mg 2 11.99 O 1230 8.00 N 1045 7.00 C 3854 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 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 301.5 milliseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 42.8% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'F' and resid 2 through 22 Processing helix chain 'F' and resid 30 through 36 removed outlier: 5.791A pdb=" N ARG F 33 " --> pdb=" O GLY F 30 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER F 34 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 52 Processing helix chain 'F' and resid 71 through 86 removed outlier: 3.631A pdb=" N GLU F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 121 through 136 removed outlier: 3.598A pdb=" N GLY F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 151 through 157 Processing helix chain 'F' and resid 165 through 186 removed outlier: 4.915A pdb=" N GLY F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 Processing helix chain 'F' and resid 269 through 281 Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 313 through 328 Processing helix chain 'G' and resid 2 through 22 Processing helix chain 'G' and resid 28 through 36 removed outlier: 3.520A pdb=" N ASP G 32 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG G 33 " --> pdb=" O GLY G 30 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER G 34 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 51 Processing helix chain 'G' and resid 71 through 86 removed outlier: 3.580A pdb=" N GLU G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 107 Processing helix chain 'G' and resid 121 through 136 removed outlier: 3.530A pdb=" N GLY G 136 " --> pdb=" O LEU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 149 Processing helix chain 'G' and resid 151 through 157 Processing helix chain 'G' and resid 165 through 186 removed outlier: 4.775A pdb=" N GLY G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 219 Processing helix chain 'G' and resid 269 through 281 Processing helix chain 'G' and resid 301 through 312 Processing helix chain 'G' and resid 312 through 328 removed outlier: 3.535A pdb=" N LEU G 328 " --> pdb=" O ARG G 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 15 through 18 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 23 removed outlier: 6.082A pdb=" N VAL B 22 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS A 133 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP A 75 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL A 131 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE A 87 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL A 130 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE A 85 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 26 through 28 removed outlier: 6.438A pdb=" N ILE G 141 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE G 192 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL G 143 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N GLN G 194 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 26 through 28 removed outlier: 6.438A pdb=" N ILE G 141 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE G 192 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL G 143 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N GLN G 194 " --> pdb=" O VAL G 143 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL G 62 " --> pdb=" O PHE G 191 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASN G 193 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE G 64 " --> pdb=" O ASN G 193 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE G 195 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY G 66 " --> pdb=" O ILE G 195 " (cutoff:3.500A) removed outlier: 9.550A pdb=" N MET G 197 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE G 61 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LEU G 223 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU G 63 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE G 225 " --> pdb=" O GLU G 63 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR G 65 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ARG G 227 " --> pdb=" O TYR G 65 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG G 222 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU G 241 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ALA G 230 " --> pdb=" O GLY G 239 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY G 239 " --> pdb=" O ALA G 230 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS G 232 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL G 237 " --> pdb=" O LYS G 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AA6, first strand: chain 'F' and resid 115 through 117 Processing sheet with id=AA7, first strand: chain 'F' and resid 115 through 117 removed outlier: 6.428A pdb=" N VAL F 62 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ASN F 193 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE F 64 " --> pdb=" O ASN F 193 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE F 195 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLY F 66 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N MET F 197 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE F 61 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU F 223 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU F 63 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE F 225 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR F 65 " --> pdb=" O ILE F 225 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ARG F 227 " --> pdb=" O TYR F 65 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL F 221 " --> pdb=" O ASN F 249 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN F 249 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU F 223 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL F 247 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE F 225 " --> pdb=" O LYS F 245 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS F 245 " --> pdb=" O ILE F 225 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ARG F 227 " --> pdb=" O ARG F 243 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG F 243 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU F 233 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 285 through 287 removed outlier: 7.096A pdb=" N TYR F 291 " --> pdb=" O ILE F 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 39 through 40 Processing sheet with id=AB1, first strand: chain 'G' and resid 285 through 287 removed outlier: 6.994A pdb=" N TYR G 291 " --> pdb=" O ILE G 298 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 900 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: 0.74 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 2059 1.36 - 1.51: 1517 1.51 - 1.65: 2635 1.65 - 1.80: 32 1.80 - 1.95: 17 Bond restraints: 6260 Sorted by residual: bond pdb=" C3' DT S 9 " pdb=" C2' DT S 9 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT S 8 " pdb=" C2' DT S 8 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.43e+00 bond pdb=" CA SER G 145 " pdb=" CB SER G 145 " ideal model delta sigma weight residual 1.532 1.498 0.033 1.36e-02 5.41e+03 5.98e+00 bond pdb=" C3' DT S 12 " pdb=" C2' DT S 12 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.64e+00 bond pdb=" N ASP G 94 " pdb=" CA ASP G 94 " ideal model delta sigma weight residual 1.462 1.490 -0.028 1.26e-02 6.30e+03 4.97e+00 ... (remaining 6255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 8229 1.33 - 2.67: 212 2.67 - 4.00: 29 4.00 - 5.33: 10 5.33 - 6.67: 1 Bond angle restraints: 8481 Sorted by residual: angle pdb=" N3 DT S 8 " pdb=" C4 DT S 8 " pdb=" O4 DT S 8 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT S 7 " pdb=" C4 DT S 7 " pdb=" O4 DT S 7 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT S 10 " pdb=" C4 DT S 10 " pdb=" O4 DT S 10 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" N3 DT S 11 " pdb=" C4 DT S 11 " pdb=" O4 DT S 11 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.62e+01 angle pdb=" N3 DT S 12 " pdb=" C4 DT S 12 " pdb=" O4 DT S 12 " ideal model delta sigma weight residual 119.90 122.28 -2.38 6.00e-01 2.78e+00 1.57e+01 ... (remaining 8476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.35: 3534 29.35 - 58.69: 231 58.69 - 88.04: 17 88.04 - 117.39: 0 117.39 - 146.74: 2 Dihedral angle restraints: 3784 sinusoidal: 1535 harmonic: 2249 Sorted by residual: dihedral pdb=" O1A AGS G 402 " pdb=" O3A AGS G 402 " pdb=" PA AGS G 402 " pdb=" PB AGS G 402 " ideal model delta sinusoidal sigma weight residual -67.73 79.01 -146.74 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" O1A AGS F 402 " pdb=" O3A AGS F 402 " pdb=" PA AGS F 402 " pdb=" PB AGS F 402 " ideal model delta sinusoidal sigma weight residual -67.73 75.30 -143.03 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" CA VAL B 34 " pdb=" C VAL B 34 " pdb=" N GLU B 35 " pdb=" CA GLU B 35 " ideal model delta harmonic sigma weight residual -180.00 -161.68 -18.32 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 686 0.036 - 0.072: 197 0.072 - 0.108: 79 0.108 - 0.144: 25 0.144 - 0.180: 2 Chirality restraints: 989 Sorted by residual: chirality pdb=" CA SER G 145 " pdb=" N SER G 145 " pdb=" C SER G 145 " pdb=" CB SER G 145 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CB THR G 208 " pdb=" CA THR G 208 " pdb=" OG1 THR G 208 " pdb=" CG2 THR G 208 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA ILE A 87 " pdb=" N ILE A 87 " pdb=" C ILE A 87 " pdb=" CB ILE A 87 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 986 not shown) Planarity restraints: 1069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 308 " 0.012 2.00e-02 2.50e+03 2.46e-02 1.51e+01 pdb=" CG TRP F 308 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP F 308 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP F 308 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 308 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP F 308 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 308 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 308 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 308 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP F 308 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 312 " -0.056 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO F 313 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO F 313 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 313 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 312 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C ASN F 312 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN F 312 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO F 313 " -0.011 2.00e-02 2.50e+03 ... (remaining 1066 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 53 2.58 - 3.16: 4740 3.16 - 3.74: 9527 3.74 - 4.32: 13337 4.32 - 4.90: 22512 Nonbonded interactions: 50169 Sorted by model distance: nonbonded pdb=" OG1 THR G 73 " pdb="MG MG G 401 " model vdw 1.995 2.170 nonbonded pdb=" O CYS B 24 " pdb=" OG SER A 60 " model vdw 2.202 3.040 nonbonded pdb=" OG SER F 44 " pdb=" OE2 GLU F 273 " model vdw 2.209 3.040 nonbonded pdb=" O GLN F 300 " pdb=" ND2 ASN F 304 " model vdw 2.243 3.120 nonbonded pdb=" O1B AGS G 402 " pdb=" O2G AGS G 402 " model vdw 2.247 3.040 ... (remaining 50164 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 'F' 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: 0.700 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.400 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.003 0.039 6260 Z= 0.182 Angle : 0.532 6.667 8481 Z= 0.350 Chirality : 0.043 0.180 989 Planarity : 0.004 0.085 1069 Dihedral : 17.863 146.736 2344 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.32 % Allowed : 17.19 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.01 (0.30), residues: 788 helix: 1.55 (0.30), residues: 317 sheet: 1.53 (0.42), residues: 132 loop : -0.52 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 134 TYR 0.026 0.001 TYR B 33 PHE 0.008 0.001 PHE A 128 TRP 0.065 0.005 TRP F 308 HIS 0.002 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.18 ( 6260) covalent geometry : angle 0.53222 / 0.35 ( 8481) hydrogen bonds : bond 0.16516 / 10.58 ( 309) hydrogen bonds : angle 7.25017 / 5.00 ( 900) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.136 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 64 average time/residue: 0.0621 time to fit residues: 5.3702 Evaluate side-chains 61 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 150 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.1980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.163776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.112941 restraints weight = 7025.924| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.98 r_work: 0.2990 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 6260 Z= 0.317 Angle : 0.659 5.626 8481 Z= 0.355 Chirality : 0.052 0.236 989 Planarity : 0.005 0.067 1069 Dihedral : 12.743 147.507 915 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.47 % Allowed : 15.93 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.43 (0.29), residues: 788 helix: 1.17 (0.29), residues: 305 sheet: 0.70 (0.40), residues: 147 loop : -0.69 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 134 TYR 0.013 0.002 TYR A 52 PHE 0.015 0.002 PHE F 255 TRP 0.032 0.004 TRP F 308 HIS 0.004 0.002 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.32 ( 6260) covalent geometry : angle 0.65921 / 0.35 ( 8481) hydrogen bonds : bond 0.04271 / 2.88 ( 309) hydrogen bonds : angle 5.64068 / 3.90 ( 900) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.204 Fit side-chains REVERT: F 203 PHE cc_start: 0.6273 (t80) cc_final: 0.5912 (t80) REVERT: G 164 MET cc_start: 0.4899 (ptm) cc_final: 0.4220 (ptm) outliers start: 22 outliers final: 16 residues processed: 73 average time/residue: 0.0609 time to fit residues: 6.2448 Evaluate side-chains 71 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 152 LYS Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.165726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.114386 restraints weight = 6959.294| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.04 r_work: 0.3003 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6260 Z= 0.178 Angle : 0.515 4.862 8481 Z= 0.284 Chirality : 0.046 0.182 989 Planarity : 0.004 0.056 1069 Dihedral : 12.422 143.317 915 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.84 % Allowed : 17.82 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.46 (0.29), residues: 788 helix: 1.09 (0.29), residues: 317 sheet: 0.85 (0.43), residues: 129 loop : -0.62 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 134 TYR 0.009 0.001 TYR A 52 PHE 0.010 0.001 PHE F 217 TRP 0.029 0.003 TRP F 308 HIS 0.001 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 6260) covalent geometry : angle 0.51480 / 0.28 ( 8481) hydrogen bonds : bond 0.03607 / 2.44 ( 309) hydrogen bonds : angle 5.35628 / 3.71 ( 900) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.139 Fit side-chains REVERT: G 159 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7941 (mm) REVERT: G 164 MET cc_start: 0.4809 (ptm) cc_final: 0.4125 (ptm) outliers start: 18 outliers final: 17 residues processed: 72 average time/residue: 0.0508 time to fit residues: 5.1910 Evaluate side-chains 74 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 67 optimal weight: 0.0980 chunk 6 optimal weight: 30.0000 chunk 40 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 4 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.167977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.117437 restraints weight = 6959.925| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.23 r_work: 0.3041 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6260 Z= 0.121 Angle : 0.458 4.449 8481 Z= 0.255 Chirality : 0.044 0.158 989 Planarity : 0.003 0.052 1069 Dihedral : 12.210 139.101 915 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.47 % Allowed : 17.67 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.67 (0.30), residues: 788 helix: 1.37 (0.30), residues: 317 sheet: 0.74 (0.42), residues: 143 loop : -0.56 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 134 TYR 0.012 0.001 TYR F 293 PHE 0.008 0.001 PHE F 217 TRP 0.029 0.002 TRP F 308 HIS 0.002 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 6260) covalent geometry : angle 0.45830 / 0.26 ( 8481) hydrogen bonds : bond 0.03115 / 2.11 ( 309) hydrogen bonds : angle 5.09867 / 3.54 ( 900) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.136 Fit side-chains REVERT: F 161 ASP cc_start: 0.8042 (m-30) cc_final: 0.7568 (m-30) REVERT: F 259 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: G 164 MET cc_start: 0.5401 (ptm) cc_final: 0.4690 (ptm) outliers start: 22 outliers final: 17 residues processed: 84 average time/residue: 0.0596 time to fit residues: 6.9268 Evaluate side-chains 79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 7.9990 chunk 60 optimal weight: 0.0980 chunk 41 optimal weight: 0.0060 chunk 69 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 37 optimal weight: 0.0070 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.171153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124543 restraints weight = 7050.897| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.74 r_work: 0.3089 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6260 Z= 0.088 Angle : 0.430 4.828 8481 Z= 0.241 Chirality : 0.043 0.157 989 Planarity : 0.003 0.049 1069 Dihedral : 12.012 134.036 915 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.00 % Allowed : 18.93 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.85 (0.30), residues: 788 helix: 1.50 (0.30), residues: 317 sheet: 0.88 (0.42), residues: 143 loop : -0.47 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 134 TYR 0.010 0.001 TYR F 271 PHE 0.014 0.001 PHE G 203 TRP 0.036 0.003 TRP F 308 HIS 0.002 0.000 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 ( 6260) covalent geometry : angle 0.43034 / 0.24 ( 8481) hydrogen bonds : bond 0.02820 / 1.94 ( 309) hydrogen bonds : angle 4.86900 / 3.38 ( 900) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.144 Fit side-chains REVERT: F 161 ASP cc_start: 0.7969 (m-30) cc_final: 0.7499 (m-30) REVERT: F 259 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: G 164 MET cc_start: 0.5346 (ptm) cc_final: 0.4717 (ptm) outliers start: 19 outliers final: 8 residues processed: 81 average time/residue: 0.0597 time to fit residues: 6.6303 Evaluate side-chains 69 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.163639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.112289 restraints weight = 7079.452| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.03 r_work: 0.3001 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6260 Z= 0.267 Angle : 0.585 5.429 8481 Z= 0.313 Chirality : 0.050 0.224 989 Planarity : 0.004 0.051 1069 Dihedral : 12.321 138.137 914 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.10 % Allowed : 17.35 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.47 (0.30), residues: 788 helix: 1.35 (0.29), residues: 305 sheet: 0.56 (0.41), residues: 143 loop : -0.72 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 134 TYR 0.012 0.001 TYR A 52 PHE 0.010 0.002 PHE F 255 TRP 0.033 0.003 TRP F 308 HIS 0.003 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.27 ( 6260) covalent geometry : angle 0.58546 / 0.31 ( 8481) hydrogen bonds : bond 0.03620 / 2.45 ( 309) hydrogen bonds : angle 5.14306 / 3.58 ( 900) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.220 Fit side-chains REVERT: B 33 TYR cc_start: 0.5024 (OUTLIER) cc_final: 0.4520 (p90) REVERT: F 259 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: G 159 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.7981 (mm) REVERT: G 164 MET cc_start: 0.5000 (ptm) cc_final: 0.4588 (ptm) outliers start: 26 outliers final: 18 residues processed: 84 average time/residue: 0.0632 time to fit residues: 7.3277 Evaluate side-chains 78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 59 optimal weight: 0.2980 chunk 50 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.169224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.119204 restraints weight = 6954.180| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.96 r_work: 0.3079 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6260 Z= 0.095 Angle : 0.439 4.421 8481 Z= 0.245 Chirality : 0.043 0.208 989 Planarity : 0.003 0.048 1069 Dihedral : 11.949 133.212 914 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.37 % Allowed : 19.09 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.71 (0.30), residues: 788 helix: 1.42 (0.30), residues: 317 sheet: 0.78 (0.42), residues: 143 loop : -0.57 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 134 TYR 0.008 0.001 TYR F 271 PHE 0.008 0.001 PHE B 15 TRP 0.043 0.003 TRP F 308 HIS 0.001 0.000 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 6260) covalent geometry : angle 0.43947 / 0.24 ( 8481) hydrogen bonds : bond 0.02798 / 1.89 ( 309) hydrogen bonds : angle 4.84501 / 3.37 ( 900) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.138 Fit side-chains REVERT: F 19 LYS cc_start: 0.8477 (ttmt) cc_final: 0.7766 (mmpt) REVERT: F 161 ASP cc_start: 0.8009 (m-30) cc_final: 0.7484 (m-30) REVERT: F 259 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: G 164 MET cc_start: 0.5365 (ptm) cc_final: 0.4703 (ptm) outliers start: 15 outliers final: 12 residues processed: 77 average time/residue: 0.0597 time to fit residues: 6.1864 Evaluate side-chains 75 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 47 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.167322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116467 restraints weight = 7033.557| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.12 r_work: 0.3033 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6260 Z= 0.140 Angle : 0.462 4.482 8481 Z= 0.254 Chirality : 0.045 0.204 989 Planarity : 0.003 0.049 1069 Dihedral : 12.015 133.594 914 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.89 % Allowed : 19.72 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.67 (0.30), residues: 788 helix: 1.41 (0.30), residues: 317 sheet: 0.74 (0.42), residues: 143 loop : -0.61 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 134 TYR 0.008 0.001 TYR A 52 PHE 0.012 0.001 PHE G 203 TRP 0.044 0.003 TRP F 308 HIS 0.003 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 6260) covalent geometry : angle 0.46233 / 0.25 ( 8481) hydrogen bonds : bond 0.02980 / 2.01 ( 309) hydrogen bonds : angle 4.86970 / 3.39 ( 900) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.176 Fit side-chains REVERT: F 19 LYS cc_start: 0.8584 (ttmt) cc_final: 0.7865 (mmpt) REVERT: F 161 ASP cc_start: 0.8093 (m-30) cc_final: 0.7579 (m-30) REVERT: F 259 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: G 164 MET cc_start: 0.4903 (ptm) cc_final: 0.4548 (ptm) outliers start: 12 outliers final: 10 residues processed: 73 average time/residue: 0.0585 time to fit residues: 5.7915 Evaluate side-chains 72 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 46 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.169983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.120802 restraints weight = 6983.547| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.23 r_work: 0.3075 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6260 Z= 0.095 Angle : 0.430 4.539 8481 Z= 0.238 Chirality : 0.043 0.165 989 Planarity : 0.003 0.047 1069 Dihedral : 11.841 132.462 914 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.37 % Allowed : 19.09 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.87 (0.30), residues: 788 helix: 1.55 (0.30), residues: 317 sheet: 0.88 (0.43), residues: 143 loop : -0.49 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 134 TYR 0.007 0.001 TYR F 271 PHE 0.010 0.001 PHE G 203 TRP 0.042 0.003 TRP F 308 HIS 0.002 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 6260) covalent geometry : angle 0.43009 / 0.24 ( 8481) hydrogen bonds : bond 0.02698 / 1.81 ( 309) hydrogen bonds : angle 4.71818 / 3.28 ( 900) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.223 Fit side-chains REVERT: F 19 LYS cc_start: 0.8527 (ttmt) cc_final: 0.7836 (mmpt) REVERT: F 161 ASP cc_start: 0.8005 (m-30) cc_final: 0.7513 (m-30) REVERT: F 259 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: G 164 MET cc_start: 0.5577 (ptm) cc_final: 0.4940 (ptm) outliers start: 15 outliers final: 12 residues processed: 77 average time/residue: 0.0627 time to fit residues: 6.7869 Evaluate side-chains 77 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.0980 chunk 8 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.170537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.121048 restraints weight = 6936.090| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.98 r_work: 0.3085 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6260 Z= 0.097 Angle : 0.427 4.278 8481 Z= 0.236 Chirality : 0.043 0.164 989 Planarity : 0.003 0.048 1069 Dihedral : 11.779 132.829 914 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.89 % Allowed : 19.24 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.90 (0.30), residues: 788 helix: 1.58 (0.30), residues: 317 sheet: 0.96 (0.45), residues: 135 loop : -0.47 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 134 TYR 0.006 0.001 TYR A 52 PHE 0.008 0.001 PHE B 18 TRP 0.038 0.002 TRP F 308 HIS 0.002 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 6260) covalent geometry : angle 0.42716 / 0.24 ( 8481) hydrogen bonds : bond 0.02684 / 1.80 ( 309) hydrogen bonds : angle 4.69080 / 3.26 ( 900) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.178 Fit side-chains REVERT: F 19 LYS cc_start: 0.8509 (ttmt) cc_final: 0.7847 (mmpt) REVERT: F 161 ASP cc_start: 0.7961 (m-30) cc_final: 0.7502 (m-30) REVERT: F 259 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: G 156 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6889 (mt-10) outliers start: 12 outliers final: 11 residues processed: 77 average time/residue: 0.0691 time to fit residues: 7.2322 Evaluate side-chains 76 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.165883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115083 restraints weight = 6974.334| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.08 r_work: 0.3006 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6260 Z= 0.204 Angle : 0.509 4.695 8481 Z= 0.276 Chirality : 0.047 0.218 989 Planarity : 0.004 0.048 1069 Dihedral : 12.095 134.510 914 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.21 % Allowed : 18.93 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.73 (0.30), residues: 788 helix: 1.54 (0.30), residues: 305 sheet: 0.87 (0.43), residues: 137 loop : -0.62 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 134 TYR 0.009 0.001 TYR A 52 PHE 0.010 0.002 PHE B 15 TRP 0.038 0.003 TRP F 308 HIS 0.003 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 ( 6260) covalent geometry : angle 0.50927 / 0.28 ( 8481) hydrogen bonds : bond 0.03264 / 2.18 ( 309) hydrogen bonds : angle 4.96736 / 3.45 ( 900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1336.13 seconds wall clock time: 23 minutes 27.76 seconds (1407.76 seconds total)