Starting phenix.real_space_refine on Tue Aug 4 22:12:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gms_34152/08_2026/8gms_34152.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gms_34152/08_2026/8gms_34152.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/8gms_34152/08_2026/8gms_34152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gms_34152/08_2026/8gms_34152.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gms_34152/08_2026/8gms_34152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gms_34152/08_2026/8gms_34152.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gms_34152/08_2026/8gms_34152.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gms_34152/08_2026/8gms_34152.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 32 5.16 5 C 4380 2.51 5 N 1218 2.21 5 O 1378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 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: 7022 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 949 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Chain: "B" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 873 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain breaks: 1 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: "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: 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: 1.29, per 1000 atoms: 0.18 Number of scatterers: 7022 At special positions: 0 Unit cell: (102.34, 116.62, 104.72, 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 32 16.00 P 12 15.00 Mg 2 11.99 O 1378 8.00 N 1218 7.00 C 4380 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: 0.63 Conformation dependent library (CDL) restraints added in 409.8 milliseconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1630 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 37.8% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.528A pdb=" N ILE A 123 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.747A pdb=" N ILE B 123 " --> pdb=" O MET B 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 22 Processing helix chain 'F' and resid 32 through 36 Processing helix chain 'F' and resid 44 through 52 Processing helix chain 'F' and resid 71 through 85 Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 121 through 136 removed outlier: 3.528A pdb=" N GLY F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 157 Processing helix chain 'F' and resid 165 through 186 removed outlier: 4.725A pdb=" N GLY F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 4.282A 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 312 through 328 removed outlier: 3.794A pdb=" N ALA F 316 " --> pdb=" O ASN F 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 22 Processing helix chain 'G' and resid 28 through 36 removed outlier: 6.237A pdb=" N ARG G 33 " --> pdb=" O GLY G 30 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER G 34 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET G 35 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP G 36 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 52 removed outlier: 3.506A pdb=" N GLY G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 removed outlier: 3.707A 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 110 through 113 Processing helix chain 'G' and resid 121 through 136 removed outlier: 3.596A 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: 4.684A pdb=" N GLY G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 4.356A 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: 3.513A pdb=" N ALA G 316 " --> pdb=" O ASN G 312 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU G 328 " --> pdb=" O ARG G 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 84 removed outlier: 3.892A pdb=" N GLY A 96 " --> pdb=" O LEU A 78 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 96 through 97 current: chain 'A' and resid 130 through 134 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 130 through 134 current: chain 'A' and resid 152 through 161 removed outlier: 3.585A pdb=" N ILE A 177 " --> pdb=" O LEU A 167 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 177 through 180 current: chain 'B' and resid 130 through 135 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 130 through 135 current: chain 'B' and resid 152 through 161 removed outlier: 3.750A pdb=" N ILE B 177 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 26 through 28 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 26 through 28 current: chain 'G' and resid 115 through 117 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 115 through 117 current: chain 'G' and resid 188 through 197 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 207 through 209 current: chain 'G' and resid 236 through 249 Processing sheet with id=AA3, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AA4, first strand: chain 'F' and resid 114 through 117 removed outlier: 7.130A pdb=" N CYS F 90 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N SER F 117 " --> pdb=" O CYS F 90 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE F 92 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE F 141 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE F 192 " --> pdb=" O ILE F 141 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL F 143 " --> pdb=" O ILE F 192 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL F 62 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASN F 193 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE F 64 " --> pdb=" O ASN F 193 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE F 61 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU F 223 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU F 63 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE F 225 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR F 65 " --> pdb=" O ILE F 225 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ARG F 227 " --> pdb=" O TYR F 65 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG F 222 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU F 241 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA F 230 " --> pdb=" O GLY F 239 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY F 239 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS F 232 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL F 237 " --> pdb=" O LYS F 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 195 through 197 Processing sheet with id=AA6, first strand: chain 'F' and resid 285 through 287 removed outlier: 6.691A pdb=" N TYR F 291 " --> pdb=" O ILE F 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 39 through 40 Processing sheet with id=AA8, first strand: chain 'G' and resid 285 through 287 removed outlier: 6.737A pdb=" N TYR G 291 " --> pdb=" O ILE G 298 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 2372 1.36 - 1.51: 1708 1.51 - 1.65: 2981 1.65 - 1.80: 36 1.80 - 1.95: 20 Bond restraints: 7117 Sorted by residual: bond pdb=" N LEU F 326 " pdb=" CA LEU F 326 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.30e-02 5.92e+03 6.27e+00 bond pdb=" C3' DT S 9 " pdb=" C2' DT S 9 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 5.97e+00 bond pdb=" C2' DT S 12 " pdb=" C1' DT S 12 " ideal model delta sigma weight residual 1.518 1.536 -0.018 1.00e-02 1.00e+04 3.10e+00 bond pdb=" C3' DT S 7 " pdb=" C2' DT S 7 " ideal model delta sigma weight residual 1.516 1.530 -0.014 8.00e-03 1.56e+04 3.09e+00 bond pdb=" C3' DT S 10 " pdb=" O3' DT S 10 " ideal model delta sigma weight residual 1.435 1.413 0.022 1.30e-02 5.92e+03 2.97e+00 ... (remaining 7112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 9407 1.85 - 3.70: 196 3.70 - 5.55: 17 5.55 - 7.41: 3 7.41 - 9.26: 1 Bond angle restraints: 9624 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 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT S 10 " pdb=" C4 DT S 10 " pdb=" O4 DT S 10 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT S 12 " pdb=" C4 DT S 12 " pdb=" O4 DT S 12 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT S 7 " pdb=" C4 DT S 7 " pdb=" O4 DT S 7 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 angle pdb=" N3 DT S 11 " pdb=" C4 DT S 11 " pdb=" O4 DT S 11 " ideal model delta sigma weight residual 119.90 122.29 -2.39 6.00e-01 2.78e+00 1.59e+01 ... (remaining 9619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 3799 21.98 - 43.96: 435 43.96 - 65.93: 78 65.93 - 87.91: 18 87.91 - 109.89: 3 Dihedral angle restraints: 4333 sinusoidal: 1790 harmonic: 2543 Sorted by residual: 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 -177.62 109.89 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" CA HIS F 163 " pdb=" C HIS F 163 " pdb=" N MET F 164 " pdb=" CA MET F 164 " ideal model delta harmonic sigma weight residual 180.00 -163.85 -16.15 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CB GLU G 154 " pdb=" CG GLU G 154 " pdb=" CD GLU G 154 " pdb=" OE1 GLU G 154 " ideal model delta sinusoidal sigma weight residual 0.00 -88.25 88.25 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 4330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 712 0.035 - 0.070: 268 0.070 - 0.106: 92 0.106 - 0.141: 39 0.141 - 0.176: 2 Chirality restraints: 1113 Sorted by residual: chirality pdb=" CB ILE B 149 " pdb=" CA ILE B 149 " pdb=" CG1 ILE B 149 " pdb=" CG2 ILE B 149 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA ASN F 205 " pdb=" N ASN F 205 " pdb=" C ASN F 205 " pdb=" CB ASN F 205 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE F 64 " pdb=" N ILE F 64 " pdb=" C ILE F 64 " pdb=" CB ILE F 64 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1110 not shown) Planarity restraints: 1225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 308 " 0.018 2.00e-02 2.50e+03 2.18e-02 1.19e+01 pdb=" CG TRP F 308 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP F 308 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP F 308 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 308 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 308 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 308 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 308 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 308 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP F 308 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 106 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 107 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 106 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 107 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 107 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 107 " 0.016 5.00e-02 4.00e+02 ... (remaining 1222 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 56 2.59 - 3.17: 5592 3.17 - 3.74: 10686 3.74 - 4.32: 14997 4.32 - 4.90: 25267 Nonbonded interactions: 56598 Sorted by model distance: nonbonded pdb="MG MG F 401 " pdb=" O2G AGS F 402 " model vdw 2.012 2.170 nonbonded pdb=" OG1 THR F 73 " pdb="MG MG F 401 " model vdw 2.022 2.170 nonbonded pdb=" OG1 THR G 73 " pdb="MG MG G 401 " model vdw 2.089 2.170 nonbonded pdb=" OG1 THR G 42 " pdb=" OD1 ASP G 48 " model vdw 2.213 3.040 nonbonded pdb=" OG SER G 44 " pdb=" OE2 GLU G 273 " model vdw 2.248 3.040 ... (remaining 56593 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 'A' and (resid 76 through 84 or resid 95 through 198)) selection = chain 'B' } 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.270 Find NCS groups from input model: 0.110 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7117 Z= 0.194 Angle : 0.627 9.258 9624 Z= 0.384 Chirality : 0.045 0.176 1113 Planarity : 0.003 0.038 1225 Dihedral : 18.591 109.890 2703 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.55 % Allowed : 19.97 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.27), residues: 892 helix: 1.47 (0.30), residues: 302 sheet: 0.43 (0.41), residues: 156 loop : -1.34 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 140 TYR 0.009 0.001 TYR F 218 PHE 0.011 0.001 PHE F 260 TRP 0.057 0.004 TRP F 308 HIS 0.003 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 ( 7117) covalent geometry : angle 0.62721 / 0.38 ( 9624) hydrogen bonds : bond 0.13885 / 8.90 ( 276) hydrogen bonds : angle 5.32660 / 3.56 ( 753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.155 Fit side-chains REVERT: B 78 LEU cc_start: 0.3521 (tp) cc_final: 0.3320 (tp) REVERT: F 280 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6742 (mttt) REVERT: F 308 TRP cc_start: 0.7043 (t60) cc_final: 0.6621 (t60) outliers start: 4 outliers final: 1 residues processed: 105 average time/residue: 0.0688 time to fit residues: 9.8453 Evaluate side-chains 103 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 240 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.0770 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.191602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142679 restraints weight = 7913.867| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.93 r_work: 0.3330 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7117 Z= 0.132 Angle : 0.508 6.735 9624 Z= 0.272 Chirality : 0.044 0.166 1113 Planarity : 0.003 0.032 1225 Dihedral : 11.080 112.793 1035 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.48 % Allowed : 19.28 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.27), residues: 892 helix: 1.56 (0.30), residues: 306 sheet: 0.44 (0.41), residues: 161 loop : -1.30 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 222 TYR 0.015 0.001 TYR F 218 PHE 0.013 0.001 PHE F 21 TRP 0.021 0.002 TRP F 308 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 7117) covalent geometry : angle 0.50815 / 0.27 ( 9624) hydrogen bonds : bond 0.03352 / 2.15 ( 276) hydrogen bonds : angle 4.35657 / 2.91 ( 753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.251 Fit side-chains REVERT: A 92 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8252 (tm-30) REVERT: A 126 MET cc_start: 0.7049 (mmm) cc_final: 0.6791 (mtp) REVERT: A 140 ARG cc_start: 0.7477 (ptt-90) cc_final: 0.6908 (ptt90) REVERT: B 78 LEU cc_start: 0.3451 (tp) cc_final: 0.3247 (tp) REVERT: B 115 VAL cc_start: 0.5125 (t) cc_final: 0.4698 (p) REVERT: B 196 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.6990 (pt) REVERT: G 326 LEU cc_start: 0.7921 (mp) cc_final: 0.7669 (mp) outliers start: 18 outliers final: 8 residues processed: 126 average time/residue: 0.0772 time to fit residues: 12.9514 Evaluate side-chains 116 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN F 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.186379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138496 restraints weight = 7977.068| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.03 r_work: 0.3232 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7117 Z= 0.220 Angle : 0.556 6.603 9624 Z= 0.295 Chirality : 0.047 0.160 1113 Planarity : 0.004 0.029 1225 Dihedral : 11.255 111.225 1031 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.41 % Allowed : 19.28 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.19 (0.27), residues: 892 helix: 1.41 (0.29), residues: 306 sheet: 0.04 (0.40), residues: 163 loop : -1.39 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 196 TYR 0.022 0.002 TYR F 218 PHE 0.014 0.002 PHE G 260 TRP 0.006 0.001 TRP F 308 HIS 0.005 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 ( 7117) covalent geometry : angle 0.55596 / 0.29 ( 9624) hydrogen bonds : bond 0.03711 / 2.35 ( 276) hydrogen bonds : angle 4.35513 / 2.93 ( 753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.200 Fit side-chains REVERT: A 92 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8277 (tm-30) REVERT: A 126 MET cc_start: 0.6927 (mmm) cc_final: 0.6632 (mtp) REVERT: A 170 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6456 (mt-10) REVERT: B 115 VAL cc_start: 0.5448 (t) cc_final: 0.5004 (p) REVERT: F 18 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5520 (tt0) REVERT: F 127 GLU cc_start: 0.7072 (pt0) cc_final: 0.6792 (pt0) REVERT: F 156 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6199 (mp0) REVERT: F 308 TRP cc_start: 0.7304 (t60) cc_final: 0.6708 (t60) REVERT: G 159 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8151 (mm) outliers start: 32 outliers final: 20 residues processed: 121 average time/residue: 0.0585 time to fit residues: 10.0972 Evaluate side-chains 121 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 202 MET Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 315 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 8 optimal weight: 0.0370 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 overall best weight: 1.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.188579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141290 restraints weight = 8002.255| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.99 r_work: 0.3261 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7117 Z= 0.116 Angle : 0.467 6.276 9624 Z= 0.253 Chirality : 0.043 0.146 1113 Planarity : 0.003 0.027 1225 Dihedral : 10.955 108.472 1031 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.13 % Allowed : 20.66 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.27), residues: 892 helix: 1.71 (0.30), residues: 306 sheet: 0.28 (0.42), residues: 156 loop : -1.39 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 157 TYR 0.021 0.001 TYR F 218 PHE 0.009 0.001 PHE F 191 TRP 0.004 0.001 TRP F 308 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 7117) covalent geometry : angle 0.46675 / 0.25 ( 9624) hydrogen bonds : bond 0.02908 / 1.89 ( 276) hydrogen bonds : angle 4.12840 / 2.77 ( 753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.161 Fit side-chains REVERT: A 92 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8257 (tm-30) REVERT: B 115 VAL cc_start: 0.5459 (t) cc_final: 0.5017 (p) REVERT: F 18 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5512 (tt0) REVERT: F 31 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: F 156 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6652 (mm-30) REVERT: F 178 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8408 (mt) REVERT: F 308 TRP cc_start: 0.7252 (t60) cc_final: 0.6747 (t60) REVERT: G 76 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8403 (m) REVERT: G 141 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8527 (mp) REVERT: G 326 LEU cc_start: 0.7916 (mp) cc_final: 0.7624 (mp) outliers start: 30 outliers final: 16 residues processed: 126 average time/residue: 0.0668 time to fit residues: 11.4581 Evaluate side-chains 119 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 242 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 12 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN B 108 ASN B 198 ASN F 269 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.186155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.138639 restraints weight = 8070.552| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.94 r_work: 0.3240 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7117 Z= 0.198 Angle : 0.533 6.462 9624 Z= 0.280 Chirality : 0.046 0.149 1113 Planarity : 0.003 0.033 1225 Dihedral : 11.099 108.219 1031 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.68 % Allowed : 20.66 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.16 (0.27), residues: 892 helix: 1.54 (0.30), residues: 306 sheet: 0.05 (0.42), residues: 159 loop : -1.44 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 176 TYR 0.009 0.001 TYR F 65 PHE 0.012 0.002 PHE G 260 TRP 0.004 0.001 TRP G 290 HIS 0.002 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 7117) covalent geometry : angle 0.53308 / 0.28 ( 9624) hydrogen bonds : bond 0.03307 / 2.14 ( 276) hydrogen bonds : angle 4.16892 / 2.82 ( 753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.157 Fit side-chains REVERT: A 92 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: B 115 VAL cc_start: 0.5613 (t) cc_final: 0.5132 (p) REVERT: B 196 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.6982 (pt) REVERT: F 18 GLU cc_start: 0.6192 (OUTLIER) cc_final: 0.5527 (tt0) REVERT: F 31 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: F 156 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6137 (mp0) REVERT: F 308 TRP cc_start: 0.7201 (t60) cc_final: 0.6839 (t60) REVERT: G 159 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8133 (mm) REVERT: G 271 TYR cc_start: 0.7565 (m-80) cc_final: 0.6926 (m-80) REVERT: G 326 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7701 (mp) outliers start: 34 outliers final: 24 residues processed: 123 average time/residue: 0.0543 time to fit residues: 9.5417 Evaluate side-chains 134 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 0.4980 chunk 88 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.187564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140507 restraints weight = 8069.966| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.03 r_work: 0.3245 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7117 Z= 0.128 Angle : 0.486 6.305 9624 Z= 0.259 Chirality : 0.044 0.136 1113 Planarity : 0.003 0.033 1225 Dihedral : 10.951 106.368 1031 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.68 % Allowed : 21.21 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.01 (0.28), residues: 892 helix: 1.72 (0.30), residues: 306 sheet: 0.19 (0.43), residues: 158 loop : -1.39 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 33 TYR 0.008 0.001 TYR F 218 PHE 0.009 0.001 PHE G 260 TRP 0.003 0.001 TRP F 290 HIS 0.003 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7117) covalent geometry : angle 0.48563 / 0.26 ( 9624) hydrogen bonds : bond 0.02929 / 1.92 ( 276) hydrogen bonds : angle 4.07607 / 2.75 ( 753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.188 Fit side-chains REVERT: A 92 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: A 157 ARG cc_start: 0.7301 (mtt-85) cc_final: 0.7041 (mtt-85) REVERT: B 115 VAL cc_start: 0.5574 (t) cc_final: 0.5097 (p) REVERT: F 18 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5509 (tt0) REVERT: F 31 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7002 (pm20) REVERT: F 156 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6994 (mm-30) REVERT: F 308 TRP cc_start: 0.7173 (t60) cc_final: 0.6797 (t60) REVERT: F 326 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6979 (tt) REVERT: G 141 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8553 (mp) REVERT: G 271 TYR cc_start: 0.7547 (m-80) cc_final: 0.6918 (m-80) REVERT: G 326 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7619 (mp) outliers start: 34 outliers final: 19 residues processed: 125 average time/residue: 0.0609 time to fit residues: 10.6798 Evaluate side-chains 128 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 8 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 171 ASN A 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.186958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140021 restraints weight = 8036.297| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.98 r_work: 0.3231 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7117 Z= 0.199 Angle : 0.533 6.483 9624 Z= 0.280 Chirality : 0.045 0.147 1113 Planarity : 0.003 0.033 1225 Dihedral : 11.049 106.976 1031 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.96 % Allowed : 21.63 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.12 (0.27), residues: 892 helix: 1.60 (0.30), residues: 306 sheet: 0.09 (0.42), residues: 158 loop : -1.45 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 33 TYR 0.009 0.001 TYR F 218 PHE 0.012 0.002 PHE F 191 TRP 0.004 0.001 TRP G 290 HIS 0.003 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 ( 7117) covalent geometry : angle 0.53290 / 0.28 ( 9624) hydrogen bonds : bond 0.03207 / 2.08 ( 276) hydrogen bonds : angle 4.12469 / 2.79 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.163 Fit side-chains REVERT: A 92 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: A 121 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6248 (pttm) REVERT: F 18 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5508 (tt0) REVERT: F 31 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: F 127 GLU cc_start: 0.6915 (pt0) cc_final: 0.6587 (pt0) REVERT: F 156 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6140 (mp0) REVERT: F 223 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8316 (mp) REVERT: F 308 TRP cc_start: 0.7170 (t60) cc_final: 0.6836 (t60) REVERT: F 326 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6871 (tt) REVERT: G 141 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8579 (mp) REVERT: G 271 TYR cc_start: 0.7583 (m-80) cc_final: 0.6980 (m-80) REVERT: G 326 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7684 (mp) outliers start: 36 outliers final: 25 residues processed: 129 average time/residue: 0.0617 time to fit residues: 11.3443 Evaluate side-chains 134 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 52 optimal weight: 0.2980 chunk 55 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 38 optimal weight: 0.1980 chunk 84 optimal weight: 0.0570 chunk 20 optimal weight: 0.4980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 ASN B 183 GLN B 184 GLN F 269 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.189191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.141991 restraints weight = 8037.439| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.99 r_work: 0.3284 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7117 Z= 0.096 Angle : 0.481 6.268 9624 Z= 0.255 Chirality : 0.043 0.128 1113 Planarity : 0.003 0.035 1225 Dihedral : 10.766 104.000 1031 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.41 % Allowed : 22.31 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.18 (0.28), residues: 892 helix: 1.93 (0.30), residues: 306 sheet: 0.30 (0.43), residues: 158 loop : -1.36 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.006 0.001 TYR F 218 PHE 0.010 0.001 PHE F 260 TRP 0.003 0.001 TRP F 308 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 7117) covalent geometry : angle 0.48104 / 0.26 ( 9624) hydrogen bonds : bond 0.02675 / 1.75 ( 276) hydrogen bonds : angle 3.99950 / 2.69 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.250 Fit side-chains REVERT: A 92 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: A 118 MET cc_start: 0.6258 (mmm) cc_final: 0.5979 (mmm) REVERT: A 121 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6706 (pttm) REVERT: A 157 ARG cc_start: 0.7341 (mtt-85) cc_final: 0.7101 (mtt-85) REVERT: A 159 LYS cc_start: 0.6506 (ttpt) cc_final: 0.6186 (ttpt) REVERT: A 171 ASN cc_start: 0.5948 (OUTLIER) cc_final: 0.5586 (t0) REVERT: F 18 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5573 (tt0) REVERT: F 31 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6971 (pm20) REVERT: F 156 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6204 (mp0) REVERT: F 178 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8410 (mt) REVERT: F 308 TRP cc_start: 0.7131 (t60) cc_final: 0.6798 (t60) REVERT: G 141 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8555 (mp) REVERT: G 271 TYR cc_start: 0.7546 (m-80) cc_final: 0.6938 (m-80) REVERT: G 326 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7648 (mp) outliers start: 32 outliers final: 15 residues processed: 123 average time/residue: 0.0672 time to fit residues: 11.6783 Evaluate side-chains 129 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.0020 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 52 optimal weight: 0.0000 chunk 9 optimal weight: 0.0050 chunk 88 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 171 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.190199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143507 restraints weight = 8007.255| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.93 r_work: 0.3298 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7117 Z= 0.098 Angle : 0.481 8.016 9624 Z= 0.252 Chirality : 0.043 0.131 1113 Planarity : 0.003 0.035 1225 Dihedral : 10.608 102.150 1031 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.13 % Allowed : 22.31 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.32 (0.28), residues: 892 helix: 2.09 (0.30), residues: 304 sheet: 0.42 (0.44), residues: 158 loop : -1.32 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.006 0.001 TYR F 65 PHE 0.008 0.001 PHE G 260 TRP 0.003 0.001 TRP F 308 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 7117) covalent geometry : angle 0.48127 / 0.25 ( 9624) hydrogen bonds : bond 0.02599 / 1.72 ( 276) hydrogen bonds : angle 3.92651 / 2.64 ( 753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.277 Fit side-chains REVERT: A 92 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: A 121 LYS cc_start: 0.6895 (ptpp) cc_final: 0.6483 (pttm) REVERT: A 171 ASN cc_start: 0.5929 (OUTLIER) cc_final: 0.5557 (t0) REVERT: F 18 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5548 (tt0) REVERT: F 156 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6076 (mp0) REVERT: F 178 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8370 (mt) REVERT: F 308 TRP cc_start: 0.7111 (t60) cc_final: 0.6778 (t60) REVERT: G 141 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8535 (mp) REVERT: G 271 TYR cc_start: 0.7541 (m-80) cc_final: 0.6942 (m-80) REVERT: G 326 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7608 (mp) outliers start: 30 outliers final: 17 residues processed: 125 average time/residue: 0.0775 time to fit residues: 13.4851 Evaluate side-chains 123 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 10 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 88 optimal weight: 9.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.190111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143476 restraints weight = 8005.377| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.98 r_work: 0.3286 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7117 Z= 0.103 Angle : 0.492 8.348 9624 Z= 0.254 Chirality : 0.043 0.132 1113 Planarity : 0.003 0.035 1225 Dihedral : 10.575 101.794 1031 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.72 % Allowed : 22.87 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.28), residues: 892 helix: 2.08 (0.31), residues: 306 sheet: 0.26 (0.43), residues: 162 loop : -1.23 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 157 TYR 0.020 0.001 TYR F 218 PHE 0.008 0.001 PHE G 260 TRP 0.003 0.001 TRP F 308 HIS 0.009 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 7117) covalent geometry : angle 0.49222 / 0.25 ( 9624) hydrogen bonds : bond 0.02567 / 1.70 ( 276) hydrogen bonds : angle 3.88714 / 2.61 ( 753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.272 Fit side-chains REVERT: A 92 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: A 118 MET cc_start: 0.6646 (mmm) cc_final: 0.6128 (mmm) REVERT: A 121 LYS cc_start: 0.6725 (OUTLIER) cc_final: 0.6343 (pttm) REVERT: A 171 ASN cc_start: 0.5968 (OUTLIER) cc_final: 0.5641 (t0) REVERT: F 18 GLU cc_start: 0.6101 (OUTLIER) cc_final: 0.5477 (tt0) REVERT: F 156 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6288 (mp0) REVERT: F 178 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8371 (mt) REVERT: F 308 TRP cc_start: 0.7108 (t60) cc_final: 0.6764 (t60) REVERT: G 271 TYR cc_start: 0.7543 (m-80) cc_final: 0.6935 (m-80) REVERT: G 326 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7593 (mp) outliers start: 27 outliers final: 18 residues processed: 112 average time/residue: 0.0704 time to fit residues: 11.2744 Evaluate side-chains 125 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 17 optimal weight: 0.0010 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.189527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142781 restraints weight = 7970.613| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.92 r_work: 0.3277 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7117 Z= 0.131 Angle : 0.507 8.255 9624 Z= 0.260 Chirality : 0.044 0.155 1113 Planarity : 0.003 0.035 1225 Dihedral : 10.635 102.480 1031 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.72 % Allowed : 22.45 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.29 (0.28), residues: 892 helix: 2.01 (0.30), residues: 306 sheet: 0.20 (0.43), residues: 165 loop : -1.22 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 157 TYR 0.011 0.001 TYR F 218 PHE 0.009 0.001 PHE G 260 TRP 0.003 0.001 TRP F 308 HIS 0.006 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7117) covalent geometry : angle 0.50708 / 0.26 ( 9624) hydrogen bonds : bond 0.02715 / 1.78 ( 276) hydrogen bonds : angle 3.89293 / 2.62 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1825.16 seconds wall clock time: 31 minutes 50.78 seconds (1910.78 seconds total)