Starting phenix.real_space_refine on Tue Aug 4 19:10:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gmt_34153/08_2026/8gmt_34153.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmt_34153/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gmt_34153/08_2026/8gmt_34153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmt_34153/08_2026/8gmt_34153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gmt_34153/08_2026/8gmt_34153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmt_34153/08_2026/8gmt_34153.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gmt_34153/08_2026/8gmt_34153.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gmt_34153/08_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 1.64, per 1000 atoms: 0.27 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: 0.33 Conformation dependent library (CDL) restraints added in 337.0 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: 0.15 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: 0.67 Time building geometry restraints manager: 0.48 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.370 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.210 ------------------------------------------------------------------------------- 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 0.53235 / 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 : 0.208 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 64 average time/residue: 0.0635 time to fit residues: 5.5790 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 : 0.212 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.163928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.112670 restraints weight = 7024.007| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.64 r_work: 0.3015 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1243 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= 0.316 Angle : 0.656 5.593 8481 Z= 0.353 Chirality : 0.052 0.234 989 Planarity : 0.005 0.067 1069 Dihedral : 12.728 147.352 915 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.31 % Allowed : 15.93 % Favored : 80.76 % 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: 1.18 (0.29), residues: 305 sheet: 0.69 (0.40), residues: 147 loop : -0.68 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 176 TYR 0.012 0.002 TYR A 52 PHE 0.015 0.002 PHE F 255 TRP 0.031 0.004 TRP F 308 HIS 0.004 0.002 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.32 ( 6260) covalent geometry : angle 0.65598 / 0.35 ( 8481) hydrogen bonds : bond 0.04263 / 2.87 ( 309) hydrogen bonds : angle 5.64301 / 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 82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.132 Fit side-chains REVERT: F 203 PHE cc_start: 0.6277 (t80) cc_final: 0.5921 (t80) REVERT: G 164 MET cc_start: 0.4816 (ptm) cc_final: 0.4158 (ptm) outliers start: 21 outliers final: 15 residues processed: 74 average time/residue: 0.0591 time to fit residues: 6.0584 Evaluate side-chains 72 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 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: 4.9990 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: 6.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.167829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.119739 restraints weight = 6941.251| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.79 r_work: 0.3046 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6260 Z= 0.125 Angle : 0.470 4.517 8481 Z= 0.263 Chirality : 0.044 0.162 989 Planarity : 0.004 0.054 1069 Dihedral : 12.263 140.957 915 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.52 % Allowed : 18.30 % Favored : 79.18 % 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: 0.62 (0.30), residues: 788 helix: 1.27 (0.30), residues: 317 sheet: 0.80 (0.41), residues: 143 loop : -0.56 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 134 TYR 0.007 0.001 TYR A 52 PHE 0.009 0.001 PHE F 217 TRP 0.030 0.002 TRP F 308 HIS 0.002 0.000 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 6260) covalent geometry : angle 0.46974 / 0.26 ( 8481) hydrogen bonds : bond 0.03339 / 2.26 ( 309) hydrogen bonds : angle 5.23958 / 3.64 ( 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 85 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.183 Fit side-chains REVERT: F 161 ASP cc_start: 0.8029 (m-30) cc_final: 0.7550 (m-30) REVERT: F 312 ASN cc_start: 0.4962 (OUTLIER) cc_final: 0.4707 (p0) REVERT: G 164 MET cc_start: 0.5370 (ptm) cc_final: 0.4639 (ptm) outliers start: 16 outliers final: 13 residues processed: 79 average time/residue: 0.0629 time to fit residues: 6.7641 Evaluate side-chains 77 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 242 THR Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 312 ASN Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 150 THR 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: 4.9990 chunk 41 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.165891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.115164 restraints weight = 6993.610| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.08 r_work: 0.3016 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6260 Z= 0.193 Angle : 0.509 4.859 8481 Z= 0.279 Chirality : 0.046 0.161 989 Planarity : 0.004 0.057 1069 Dihedral : 12.301 140.828 915 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.94 % Allowed : 17.19 % 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: 0.50 (0.30), residues: 788 helix: 1.22 (0.30), residues: 317 sheet: 0.62 (0.41), residues: 143 loop : -0.62 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 134 TYR 0.010 0.001 TYR A 52 PHE 0.009 0.002 PHE F 217 TRP 0.032 0.002 TRP F 308 HIS 0.003 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 ( 6260) covalent geometry : angle 0.50936 / 0.28 ( 8481) hydrogen bonds : bond 0.03421 / 2.32 ( 309) hydrogen bonds : angle 5.19833 / 3.61 ( 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 85 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.163 Fit side-chains REVERT: F 259 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: G 159 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.7974 (mm) REVERT: G 164 MET cc_start: 0.4863 (ptm) cc_final: 0.4155 (ptm) outliers start: 25 outliers final: 19 residues processed: 80 average time/residue: 0.0665 time to fit residues: 7.2982 Evaluate side-chains 80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 0.4980 chunk 60 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.169568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.118739 restraints weight = 7064.468| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.05 r_work: 0.3054 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1564 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= 0.107 Angle : 0.446 4.642 8481 Z= 0.248 Chirality : 0.043 0.156 989 Planarity : 0.003 0.057 1069 Dihedral : 12.118 136.574 915 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.15 % Allowed : 17.67 % Favored : 79.18 % 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: 0.75 (0.30), residues: 788 helix: 1.42 (0.30), residues: 317 sheet: 0.99 (0.44), residues: 129 loop : -0.54 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 134 TYR 0.008 0.001 TYR F 271 PHE 0.008 0.001 PHE F 217 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 0.00242 / 0.11 ( 6260) covalent geometry : angle 0.44647 / 0.25 ( 8481) hydrogen bonds : bond 0.02946 / 1.99 ( 309) hydrogen bonds : angle 4.98268 / 3.47 ( 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 84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.230 Fit side-chains REVERT: F 161 ASP cc_start: 0.8018 (m-30) cc_final: 0.7548 (m-30) REVERT: F 259 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: G 164 MET cc_start: 0.5425 (ptm) cc_final: 0.4769 (ptm) outliers start: 20 outliers final: 10 residues processed: 78 average time/residue: 0.0695 time to fit residues: 7.3635 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 : 0.132 ------------------------------------------------------------------------------- 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 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 259 GLU 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 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: 9.9990 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 0.0370 chunk 32 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.1862 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.168666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121476 restraints weight = 6991.495| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.84 r_work: 0.3034 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6260 Z= 0.125 Angle : 0.455 4.403 8481 Z= 0.250 Chirality : 0.044 0.207 989 Planarity : 0.003 0.053 1069 Dihedral : 12.094 135.920 914 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.15 % Allowed : 17.67 % Favored : 79.18 % 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: 0.72 (0.30), residues: 788 helix: 1.44 (0.30), residues: 317 sheet: 0.77 (0.42), residues: 143 loop : -0.57 (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 0.007 0.001 PHE F 217 TRP 0.036 0.003 TRP F 308 HIS 0.002 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 6260) covalent geometry : angle 0.45495 / 0.25 ( 8481) hydrogen bonds : bond 0.02961 / 2.01 ( 309) hydrogen bonds : angle 4.93205 / 3.43 ( 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 87 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.167 Fit side-chains REVERT: F 161 ASP cc_start: 0.8060 (m-30) cc_final: 0.7542 (m-30) REVERT: F 259 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: G 159 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7839 (mm) REVERT: G 164 MET cc_start: 0.5429 (ptm) cc_final: 0.4779 (ptm) outliers start: 20 outliers final: 15 residues processed: 82 average time/residue: 0.0643 time to fit residues: 7.2246 Evaluate side-chains 78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 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 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: 7.9990 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 13 optimal weight: 10.0000 chunk 59 optimal weight: 0.0040 chunk 50 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.168884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.123487 restraints weight = 6946.178| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.87 r_work: 0.3053 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1775 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= 0.103 Angle : 0.435 4.455 8481 Z= 0.240 Chirality : 0.043 0.163 989 Planarity : 0.003 0.051 1069 Dihedral : 11.999 133.565 914 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.84 % Allowed : 18.14 % Favored : 79.02 % 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: 0.82 (0.30), residues: 788 helix: 1.52 (0.30), residues: 317 sheet: 0.86 (0.42), residues: 143 loop : -0.54 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 134 TYR 0.008 0.001 TYR F 271 PHE 0.007 0.001 PHE B 15 TRP 0.041 0.003 TRP F 308 HIS 0.002 0.000 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 6260) covalent geometry : angle 0.43542 / 0.24 ( 8481) hydrogen bonds : bond 0.02804 / 1.90 ( 309) hydrogen bonds : angle 4.80643 / 3.34 ( 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 84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.205 Fit side-chains REVERT: F 19 LYS cc_start: 0.8515 (ttmt) cc_final: 0.7688 (mmpt) REVERT: F 161 ASP cc_start: 0.8009 (m-30) cc_final: 0.7490 (m-30) REVERT: F 259 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: G 164 MET cc_start: 0.5423 (ptm) cc_final: 0.4754 (ptm) outliers start: 18 outliers final: 15 residues processed: 80 average time/residue: 0.0667 time to fit residues: 7.3041 Evaluate side-chains 81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 150 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 326 LEU 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 162 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.165810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.114033 restraints weight = 7055.487| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.07 r_work: 0.3023 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6260 Z= 0.194 Angle : 0.506 4.809 8481 Z= 0.274 Chirality : 0.047 0.207 989 Planarity : 0.004 0.051 1069 Dihedral : 12.125 134.920 914 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.15 % Allowed : 17.98 % 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: 1.58 (0.30), residues: 305 sheet: 0.63 (0.42), residues: 143 loop : -0.67 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 134 TYR 0.010 0.001 TYR A 52 PHE 0.011 0.002 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 0.00459 / 0.19 ( 6260) covalent geometry : angle 0.50575 / 0.27 ( 8481) hydrogen bonds : bond 0.03245 / 2.19 ( 309) hydrogen bonds : angle 4.97554 / 3.46 ( 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 84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.225 Fit side-chains REVERT: F 259 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: G 159 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7912 (mm) REVERT: G 164 MET cc_start: 0.4918 (ptm) cc_final: 0.4554 (ptm) outliers start: 20 outliers final: 16 residues processed: 79 average time/residue: 0.0635 time to fit residues: 6.9679 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 : 0.221 ------------------------------------------------------------------------------- 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 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 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 195 ILE 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: 2.9990 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 chunk 46 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.169052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.119639 restraints weight = 6999.051| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.09 r_work: 0.3059 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6260 Z= 0.101 Angle : 0.442 4.630 8481 Z= 0.244 Chirality : 0.043 0.177 989 Planarity : 0.003 0.052 1069 Dihedral : 11.924 132.879 914 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.84 % Allowed : 18.61 % 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: 0.78 (0.30), residues: 788 helix: 1.51 (0.30), residues: 317 sheet: 0.76 (0.42), residues: 143 loop : -0.54 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 134 TYR 0.007 0.001 TYR F 271 PHE 0.010 0.001 PHE G 203 TRP 0.043 0.003 TRP F 308 HIS 0.002 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 6260) covalent geometry : angle 0.44244 / 0.24 ( 8481) hydrogen bonds : bond 0.02795 / 1.87 ( 309) hydrogen bonds : angle 4.80805 / 3.35 ( 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 81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.228 Fit side-chains REVERT: F 19 LYS cc_start: 0.8465 (ttmt) cc_final: 0.7759 (mmpt) REVERT: F 161 ASP cc_start: 0.8039 (m-30) cc_final: 0.7521 (m-30) REVERT: F 259 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: G 164 MET cc_start: 0.5411 (ptm) cc_final: 0.4761 (ptm) REVERT: G 202 MET cc_start: 0.6594 (mtp) cc_final: 0.5823 (mmt) outliers start: 18 outliers final: 15 residues processed: 77 average time/residue: 0.0832 time to fit residues: 8.7191 Evaluate side-chains 78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 111 ILE Chi-restraints excluded: chain F residue 146 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.0060 chunk 8 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.169664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.119458 restraints weight = 6953.951| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.96 r_work: 0.3077 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2031 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= 0.103 Angle : 0.436 4.219 8481 Z= 0.240 Chirality : 0.043 0.153 989 Planarity : 0.003 0.052 1069 Dihedral : 11.876 133.498 914 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.68 % Allowed : 18.45 % 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: 0.88 (0.30), residues: 788 helix: 1.55 (0.30), residues: 317 sheet: 1.07 (0.46), residues: 129 loop : -0.50 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 134 TYR 0.007 0.001 TYR A 52 PHE 0.009 0.001 PHE B 18 TRP 0.042 0.003 TRP F 308 HIS 0.003 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 6260) covalent geometry : angle 0.43645 / 0.24 ( 8481) hydrogen bonds : bond 0.02757 / 1.84 ( 309) hydrogen bonds : angle 4.74088 / 3.30 ( 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 80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.138 Fit side-chains REVERT: F 19 LYS cc_start: 0.8542 (ttmt) cc_final: 0.7843 (mmpt) REVERT: F 161 ASP cc_start: 0.8009 (m-30) cc_final: 0.7512 (m-30) REVERT: F 259 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: G 156 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6689 (mt-10) REVERT: G 164 MET cc_start: 0.5488 (ptm) cc_final: 0.4850 (ptm) outliers start: 17 outliers final: 16 residues processed: 76 average time/residue: 0.0632 time to fit residues: 6.6211 Evaluate side-chains 80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 111 ILE 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.166429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.111052 restraints weight = 6958.078| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.80 r_work: 0.3021 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6260 Z= 0.187 Angle : 0.500 4.659 8481 Z= 0.271 Chirality : 0.046 0.219 989 Planarity : 0.004 0.051 1069 Dihedral : 12.110 134.351 914 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.00 % Allowed : 18.45 % 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: 0.74 (0.30), residues: 788 helix: 1.62 (0.30), residues: 305 sheet: 0.66 (0.42), residues: 143 loop : -0.60 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 134 TYR 0.008 0.001 TYR A 52 PHE 0.010 0.002 PHE B 15 TRP 0.042 0.003 TRP F 308 HIS 0.003 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 ( 6260) covalent geometry : angle 0.49998 / 0.27 ( 8481) hydrogen bonds : bond 0.03205 / 2.14 ( 309) hydrogen bonds : angle 4.93583 / 3.44 ( 900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1494.69 seconds wall clock time: 26 minutes 12.32 seconds (1572.32 seconds total)