Starting phenix.real_space_refine on Wed Mar 4 01:42:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7agf_11778/03_2026/7agf_11778.cif Found real_map, /net/cci-nas-00/data/ceres_data/7agf_11778/03_2026/7agf_11778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7agf_11778/03_2026/7agf_11778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7agf_11778/03_2026/7agf_11778.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7agf_11778/03_2026/7agf_11778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7agf_11778/03_2026/7agf_11778.map" } resolution = 3.1 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 6354 2.51 5 N 1641 2.21 5 O 2040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10071 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "D" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1819 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Restraints were copied for chains: B, C, E, F Time building chain proxies: 1.95, per 1000 atoms: 0.19 Number of scatterers: 10071 At special positions: 0 Unit cell: (126.75, 131.3, 98.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 2040 8.00 N 1641 7.00 C 6354 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: 0.64 Conformation dependent library (CDL) restraints added in 370.9 milliseconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 24 sheets defined 7.2% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.852A pdb=" N GLU A 250 " --> pdb=" O ASN A 247 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 296 removed outlier: 3.576A pdb=" N MET D 296 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 296 removed outlier: 3.577A pdb=" N MET E 296 " --> pdb=" O TYR E 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 296 removed outlier: 3.578A pdb=" N MET F 296 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 246 through 252 removed outlier: 3.852A pdb=" N GLU B 250 " --> pdb=" O ASN B 247 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.852A pdb=" N GLU C 250 " --> pdb=" O ASN C 247 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 135 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 199 removed outlier: 5.609A pdb=" N ASN A 297 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA4, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.316A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR D 187 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU D 154 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR D 189 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.698A pdb=" N LEU D 128 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR D 173 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 242 through 245 removed outlier: 4.165A pdb=" N THR D 242 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 259 through 265 removed outlier: 6.735A pdb=" N SER D 302 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AB1, first strand: chain 'E' and resid 114 through 120 removed outlier: 6.315A pdb=" N PHE E 115 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG E 212 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY E 117 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU E 214 " --> pdb=" O GLY E 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E 119 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR E 187 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU E 154 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR E 189 " --> pdb=" O VAL E 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 131 removed outlier: 6.698A pdb=" N LEU E 128 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR E 173 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 242 through 245 removed outlier: 4.164A pdb=" N THR E 242 " --> pdb=" O VAL E 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 259 through 265 removed outlier: 6.734A pdb=" N SER E 302 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 109 through 110 Processing sheet with id=AB6, first strand: chain 'F' and resid 114 through 120 removed outlier: 6.315A pdb=" N PHE F 115 " --> pdb=" O GLN F 210 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG F 212 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY F 117 " --> pdb=" O ARG F 212 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU F 214 " --> pdb=" O GLY F 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL F 119 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR F 187 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU F 154 " --> pdb=" O THR F 187 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR F 189 " --> pdb=" O VAL F 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 128 through 131 removed outlier: 6.698A pdb=" N LEU F 128 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR F 173 " --> pdb=" O LEU F 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 242 through 245 removed outlier: 4.165A pdb=" N THR F 242 " --> pdb=" O VAL F 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 259 through 265 removed outlier: 6.735A pdb=" N SER F 302 " --> pdb=" O ALA F 264 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 133 through 135 Processing sheet with id=AC2, first strand: chain 'B' and resid 190 through 199 removed outlier: 5.608A pdb=" N ASN B 297 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AC4, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AC5, first strand: chain 'C' and resid 190 through 199 removed outlier: 5.608A pdb=" N ASN C 297 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 219 through 220 258 hydrogen bonds defined for protein. 630 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: 1.48 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3318 1.34 - 1.46: 2243 1.46 - 1.58: 4648 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 10269 Sorted by residual: bond pdb=" CD ARG E 180 " pdb=" NE ARG E 180 " ideal model delta sigma weight residual 1.458 1.433 0.025 1.40e-02 5.10e+03 3.21e+00 bond pdb=" CD ARG D 180 " pdb=" NE ARG D 180 " ideal model delta sigma weight residual 1.458 1.433 0.025 1.40e-02 5.10e+03 3.19e+00 bond pdb=" CD ARG F 180 " pdb=" NE ARG F 180 " ideal model delta sigma weight residual 1.458 1.434 0.024 1.40e-02 5.10e+03 2.99e+00 bond pdb=" CZ ARG D 180 " pdb=" NH2 ARG D 180 " ideal model delta sigma weight residual 1.330 1.308 0.022 1.30e-02 5.92e+03 2.98e+00 bond pdb=" CZ ARG E 180 " pdb=" NH2 ARG E 180 " ideal model delta sigma weight residual 1.330 1.308 0.022 1.30e-02 5.92e+03 2.77e+00 ... (remaining 10264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 13622 2.26 - 4.51: 316 4.51 - 6.77: 57 6.77 - 9.03: 9 9.03 - 11.28: 6 Bond angle restraints: 14010 Sorted by residual: angle pdb=" C ARG D 316 " pdb=" N SER D 317 " pdb=" CA SER D 317 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C ARG F 316 " pdb=" N SER F 317 " pdb=" CA SER F 317 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C ARG E 316 " pdb=" N SER E 317 " pdb=" CA SER E 317 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C ILE E 284 " pdb=" N VAL E 285 " pdb=" CA VAL E 285 " ideal model delta sigma weight residual 122.91 117.62 5.29 1.43e+00 4.89e-01 1.37e+01 angle pdb=" C ILE D 284 " pdb=" N VAL D 285 " pdb=" CA VAL D 285 " ideal model delta sigma weight residual 122.91 117.63 5.28 1.43e+00 4.89e-01 1.36e+01 ... (remaining 14005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.86: 5603 15.86 - 31.72: 414 31.72 - 47.58: 87 47.58 - 63.44: 25 63.44 - 79.30: 15 Dihedral angle restraints: 6144 sinusoidal: 2352 harmonic: 3792 Sorted by residual: dihedral pdb=" CA SER E 153 " pdb=" C SER E 153 " pdb=" N LEU E 154 " pdb=" CA LEU E 154 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA SER F 153 " pdb=" C SER F 153 " pdb=" N LEU F 154 " pdb=" CA LEU F 154 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA SER D 153 " pdb=" C SER D 153 " pdb=" N LEU D 154 " pdb=" CA LEU D 154 " ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 6141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 922 0.040 - 0.081: 514 0.081 - 0.121: 163 0.121 - 0.161: 44 0.161 - 0.201: 10 Chirality restraints: 1653 Sorted by residual: chirality pdb=" CA GLU E 155 " pdb=" N GLU E 155 " pdb=" C GLU E 155 " pdb=" CB GLU E 155 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLU F 155 " pdb=" N GLU F 155 " pdb=" C GLU F 155 " pdb=" CB GLU F 155 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLU D 155 " pdb=" N GLU D 155 " pdb=" C GLU D 155 " pdb=" CB GLU D 155 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 1650 not shown) Planarity restraints: 1815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 135 " -0.043 2.00e-02 2.50e+03 4.82e-02 5.81e+01 pdb=" CG TRP A 135 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP A 135 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP A 135 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 135 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 135 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 135 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 135 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 135 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A 135 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 135 " -0.043 2.00e-02 2.50e+03 4.82e-02 5.80e+01 pdb=" CG TRP C 135 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP C 135 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP C 135 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 135 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 135 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP C 135 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 135 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 135 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP C 135 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 135 " 0.042 2.00e-02 2.50e+03 4.82e-02 5.80e+01 pdb=" CG TRP B 135 " -0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP B 135 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP B 135 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 135 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 135 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 135 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 135 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 135 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP B 135 " 0.003 2.00e-02 2.50e+03 ... (remaining 1812 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 295 2.69 - 3.24: 9486 3.24 - 3.79: 16487 3.79 - 4.35: 22330 4.35 - 4.90: 36442 Nonbonded interactions: 85040 Sorted by model distance: nonbonded pdb=" OH TYR A 319 " pdb=" OH TYR C 319 " model vdw 2.136 3.040 nonbonded pdb=" OH TYR A 319 " pdb=" OH TYR B 319 " model vdw 2.142 3.040 nonbonded pdb=" OH TYR B 319 " pdb=" OH TYR C 319 " model vdw 2.145 3.040 nonbonded pdb=" OE1 GLU D 170 " pdb=" OH TYR D 172 " model vdw 2.244 3.040 nonbonded pdb=" OE1 GLU E 170 " pdb=" OH TYR E 172 " model vdw 2.244 3.040 ... (remaining 85035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.600 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: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.070 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.006 0.050 10269 Z= 0.287 Angle : 0.878 11.283 14010 Z= 0.489 Chirality : 0.054 0.201 1653 Planarity : 0.005 0.048 1815 Dihedral : 13.216 79.297 3684 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.24), residues: 1275 helix: -3.96 (0.41), residues: 36 sheet: -0.79 (0.24), residues: 453 loop : -0.36 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG D 180 TYR 0.023 0.002 TYR C 174 PHE 0.019 0.003 PHE D 301 TRP 0.123 0.011 TRP A 135 HIS 0.004 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00635 (10269) covalent geometry : angle 0.87819 (14010) hydrogen bonds : bond 0.14312 ( 258) hydrogen bonds : angle 8.59801 ( 630) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 300 ASP cc_start: 0.6668 (t0) cc_final: 0.6405 (t0) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1171 time to fit residues: 39.4744 Evaluate side-chains 182 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.0070 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN D 165 ASN D 238 ASN D 279 GLN E 165 ASN E 219 ASN E 238 ASN E 279 GLN F 165 ASN F 238 ASN F 279 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.103358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.068511 restraints weight = 20100.131| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.44 r_work: 0.2790 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10269 Z= 0.149 Angle : 0.613 8.629 14010 Z= 0.323 Chirality : 0.046 0.145 1653 Planarity : 0.004 0.036 1815 Dihedral : 5.455 21.463 1365 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.31 % Allowed : 7.24 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1275 helix: -3.80 (0.50), residues: 36 sheet: -0.91 (0.23), residues: 468 loop : -0.24 (0.24), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 193 TYR 0.025 0.001 TYR D 319 PHE 0.018 0.002 PHE D 301 TRP 0.032 0.004 TRP C 135 HIS 0.002 0.000 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00336 (10269) covalent geometry : angle 0.61313 (14010) hydrogen bonds : bond 0.03577 ( 258) hydrogen bonds : angle 7.08300 ( 630) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7297 (mm-40) REVERT: D 271 TYR cc_start: 0.6587 (m-80) cc_final: 0.6142 (m-80) REVERT: B 250 GLU cc_start: 0.8826 (pt0) cc_final: 0.8600 (pt0) REVERT: B 323 GLU cc_start: 0.8673 (tp30) cc_final: 0.8023 (tp30) REVERT: C 250 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: C 323 GLU cc_start: 0.8669 (tp30) cc_final: 0.8092 (tp30) outliers start: 15 outliers final: 12 residues processed: 193 average time/residue: 0.1093 time to fit residues: 28.3049 Evaluate side-chains 184 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 272 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 101 optimal weight: 0.0470 chunk 75 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 34 optimal weight: 0.0000 chunk 122 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 80 optimal weight: 0.0970 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN B 297 ASN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.104104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.069373 restraints weight = 19958.450| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.44 r_work: 0.2807 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10269 Z= 0.113 Angle : 0.550 7.974 14010 Z= 0.294 Chirality : 0.046 0.152 1653 Planarity : 0.003 0.026 1815 Dihedral : 4.984 18.057 1365 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.13 % Allowed : 8.46 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.25), residues: 1275 helix: -3.52 (0.58), residues: 36 sheet: -0.79 (0.23), residues: 468 loop : -0.09 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 280 TYR 0.012 0.001 TYR E 149 PHE 0.020 0.002 PHE D 301 TRP 0.023 0.003 TRP B 135 HIS 0.001 0.000 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00250 (10269) covalent geometry : angle 0.54999 (14010) hydrogen bonds : bond 0.03300 ( 258) hydrogen bonds : angle 6.74369 ( 630) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 TYR cc_start: 0.8870 (m-80) cc_final: 0.8524 (m-80) REVERT: D 210 GLN cc_start: 0.8784 (mp10) cc_final: 0.8387 (mp10) REVERT: D 271 TYR cc_start: 0.6496 (m-80) cc_final: 0.6192 (m-80) REVERT: B 250 GLU cc_start: 0.8862 (pt0) cc_final: 0.8632 (pt0) REVERT: B 276 MET cc_start: 0.8489 (mtm) cc_final: 0.8238 (mtm) REVERT: B 323 GLU cc_start: 0.8685 (tp30) cc_final: 0.8130 (tp30) REVERT: C 236 MET cc_start: 0.9371 (mmp) cc_final: 0.9084 (mmt) REVERT: C 250 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8403 (pt0) REVERT: C 319 TYR cc_start: 0.8963 (m-80) cc_final: 0.8683 (m-80) REVERT: C 323 GLU cc_start: 0.8691 (tp30) cc_final: 0.8141 (tp30) outliers start: 13 outliers final: 5 residues processed: 190 average time/residue: 0.1194 time to fit residues: 30.5311 Evaluate side-chains 176 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 170 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 272 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 102 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 279 GLN E 279 GLN F 219 ASN B 231 ASN C 231 ASN C 297 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.101590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.066783 restraints weight = 20152.666| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.46 r_work: 0.2759 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10269 Z= 0.174 Angle : 0.571 8.194 14010 Z= 0.304 Chirality : 0.047 0.173 1653 Planarity : 0.003 0.031 1815 Dihedral : 4.960 17.354 1365 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.09 % Allowed : 9.95 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1275 helix: -3.17 (0.63), residues: 36 sheet: -0.67 (0.24), residues: 468 loop : -0.02 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 193 TYR 0.013 0.002 TYR E 149 PHE 0.019 0.002 PHE F 301 TRP 0.021 0.003 TRP C 135 HIS 0.002 0.000 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00396 (10269) covalent geometry : angle 0.57146 (14010) hydrogen bonds : bond 0.03318 ( 258) hydrogen bonds : angle 6.54931 ( 630) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.8856 (pt0) cc_final: 0.8518 (pt0) REVERT: A 276 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8015 (mtm) REVERT: A 319 TYR cc_start: 0.8895 (m-80) cc_final: 0.8487 (m-80) REVERT: D 112 GLN cc_start: 0.8468 (pm20) cc_final: 0.8248 (pm20) REVERT: D 143 LEU cc_start: 0.8353 (pt) cc_final: 0.8098 (tp) REVERT: D 210 GLN cc_start: 0.8756 (mp10) cc_final: 0.8367 (mp10) REVERT: D 271 TYR cc_start: 0.6696 (m-80) cc_final: 0.6395 (m-80) REVERT: F 210 GLN cc_start: 0.8477 (mp10) cc_final: 0.7953 (mp10) REVERT: B 181 ASP cc_start: 0.9145 (OUTLIER) cc_final: 0.8913 (t0) REVERT: B 250 GLU cc_start: 0.8901 (pt0) cc_final: 0.8671 (pt0) REVERT: B 323 GLU cc_start: 0.8745 (tp30) cc_final: 0.8121 (tp30) REVERT: C 236 MET cc_start: 0.9402 (mmp) cc_final: 0.9154 (mmt) REVERT: C 250 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8423 (pt0) REVERT: C 276 MET cc_start: 0.8461 (ttm) cc_final: 0.8174 (mtp) REVERT: C 319 TYR cc_start: 0.8795 (m-80) cc_final: 0.8555 (m-80) REVERT: C 323 GLU cc_start: 0.8732 (tp30) cc_final: 0.8120 (tp30) outliers start: 24 outliers final: 11 residues processed: 184 average time/residue: 0.1140 time to fit residues: 28.2620 Evaluate side-chains 181 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 99 optimal weight: 3.9990 chunk 97 optimal weight: 0.0270 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 120 optimal weight: 0.1980 chunk 107 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.102346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.067613 restraints weight = 20240.600| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.49 r_work: 0.2780 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10269 Z= 0.141 Angle : 0.553 8.096 14010 Z= 0.297 Chirality : 0.046 0.180 1653 Planarity : 0.003 0.026 1815 Dihedral : 4.805 17.537 1365 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.66 % Allowed : 10.03 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.25), residues: 1275 helix: -2.85 (0.70), residues: 36 sheet: -0.52 (0.24), residues: 462 loop : -0.09 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 193 TYR 0.014 0.001 TYR E 149 PHE 0.020 0.002 PHE F 301 TRP 0.016 0.003 TRP C 296 HIS 0.001 0.000 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00317 (10269) covalent geometry : angle 0.55322 (14010) hydrogen bonds : bond 0.03194 ( 258) hydrogen bonds : angle 6.51773 ( 630) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.8852 (pt0) cc_final: 0.8481 (pt0) REVERT: A 276 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8228 (mtm) REVERT: A 291 ARG cc_start: 0.8495 (ttm-80) cc_final: 0.8262 (ttm-80) REVERT: A 323 GLU cc_start: 0.8906 (tp30) cc_final: 0.8699 (mm-30) REVERT: D 112 GLN cc_start: 0.8504 (pm20) cc_final: 0.8263 (pm20) REVERT: D 143 LEU cc_start: 0.8363 (pt) cc_final: 0.8114 (tp) REVERT: D 210 GLN cc_start: 0.8764 (mp10) cc_final: 0.8379 (mp10) REVERT: D 271 TYR cc_start: 0.6782 (m-80) cc_final: 0.6427 (m-80) REVERT: F 112 GLN cc_start: 0.8453 (pm20) cc_final: 0.8222 (pm20) REVERT: F 210 GLN cc_start: 0.8517 (mp10) cc_final: 0.7982 (mp10) REVERT: B 181 ASP cc_start: 0.9156 (OUTLIER) cc_final: 0.8938 (t0) REVERT: B 250 GLU cc_start: 0.8911 (pt0) cc_final: 0.8677 (pt0) REVERT: B 276 MET cc_start: 0.8536 (mtm) cc_final: 0.8190 (mtp) REVERT: B 319 TYR cc_start: 0.9047 (m-80) cc_final: 0.8838 (m-80) REVERT: B 323 GLU cc_start: 0.8750 (tp30) cc_final: 0.8132 (tp30) REVERT: C 250 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8458 (pt0) REVERT: C 323 GLU cc_start: 0.8713 (tp30) cc_final: 0.8140 (tp30) outliers start: 19 outliers final: 12 residues processed: 182 average time/residue: 0.1177 time to fit residues: 28.8512 Evaluate side-chains 182 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 272 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 49 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** 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 = 0.3540 r_free = 0.3540 target = 0.101463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.066746 restraints weight = 20214.735| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.48 r_work: 0.2760 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10269 Z= 0.155 Angle : 0.559 8.127 14010 Z= 0.300 Chirality : 0.046 0.177 1653 Planarity : 0.003 0.025 1815 Dihedral : 4.782 17.326 1365 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.01 % Allowed : 10.12 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.25), residues: 1275 helix: -2.58 (0.76), residues: 36 sheet: -0.51 (0.24), residues: 462 loop : -0.10 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 193 TYR 0.015 0.001 TYR E 149 PHE 0.022 0.002 PHE D 301 TRP 0.016 0.003 TRP B 296 HIS 0.001 0.000 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00352 (10269) covalent geometry : angle 0.55933 (14010) hydrogen bonds : bond 0.03174 ( 258) hydrogen bonds : angle 6.43175 ( 630) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.8867 (pt0) cc_final: 0.8488 (pt0) REVERT: A 276 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8442 (ttm) REVERT: A 291 ARG cc_start: 0.8548 (ttm-80) cc_final: 0.8206 (ttm-80) REVERT: A 319 TYR cc_start: 0.8748 (m-80) cc_final: 0.8495 (m-80) REVERT: D 112 GLN cc_start: 0.8495 (pm20) cc_final: 0.8243 (pm20) REVERT: D 210 GLN cc_start: 0.8763 (mp10) cc_final: 0.8367 (mp10) REVERT: D 271 TYR cc_start: 0.6974 (m-80) cc_final: 0.6632 (m-80) REVERT: F 112 GLN cc_start: 0.8454 (pm20) cc_final: 0.8201 (pm20) REVERT: F 210 GLN cc_start: 0.8530 (mp10) cc_final: 0.7980 (mp10) REVERT: B 181 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8948 (t0) REVERT: B 250 GLU cc_start: 0.8899 (pt0) cc_final: 0.8664 (pt0) REVERT: B 276 MET cc_start: 0.8535 (mtm) cc_final: 0.8306 (mtp) REVERT: B 319 TYR cc_start: 0.8984 (m-80) cc_final: 0.8776 (m-80) REVERT: B 323 GLU cc_start: 0.8754 (tp30) cc_final: 0.8104 (tp30) REVERT: C 196 GLU cc_start: 0.8387 (tp30) cc_final: 0.7943 (tp30) REVERT: C 250 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8439 (pt0) REVERT: C 276 MET cc_start: 0.8546 (mtp) cc_final: 0.8235 (mtm) REVERT: C 291 ARG cc_start: 0.8611 (ttm-80) cc_final: 0.8187 (ttm-80) REVERT: C 323 GLU cc_start: 0.8736 (tp30) cc_final: 0.8151 (tp30) outliers start: 23 outliers final: 18 residues processed: 185 average time/residue: 0.1113 time to fit residues: 27.8817 Evaluate side-chains 191 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 77 optimal weight: 0.0870 chunk 19 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 231 ASN C 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.097995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.063633 restraints weight = 20433.719| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.44 r_work: 0.2699 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 10269 Z= 0.297 Angle : 0.647 9.453 14010 Z= 0.342 Chirality : 0.049 0.242 1653 Planarity : 0.003 0.028 1815 Dihedral : 5.231 20.882 1365 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.44 % Allowed : 10.99 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.24), residues: 1275 helix: -3.52 (0.56), residues: 54 sheet: -0.60 (0.24), residues: 456 loop : -0.28 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 193 TYR 0.016 0.002 TYR E 149 PHE 0.024 0.002 PHE F 301 TRP 0.022 0.003 TRP A 296 HIS 0.003 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00684 (10269) covalent geometry : angle 0.64687 (14010) hydrogen bonds : bond 0.03518 ( 258) hydrogen bonds : angle 6.56300 ( 630) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8266 (tp30) cc_final: 0.7623 (tp30) REVERT: A 291 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8025 (ttm-80) REVERT: D 271 TYR cc_start: 0.6985 (m-80) cc_final: 0.6620 (m-80) REVERT: F 112 GLN cc_start: 0.8368 (pm20) cc_final: 0.8068 (pm20) REVERT: F 210 GLN cc_start: 0.8469 (mp10) cc_final: 0.7899 (mp10) REVERT: B 181 ASP cc_start: 0.9182 (OUTLIER) cc_final: 0.8978 (t0) REVERT: B 276 MET cc_start: 0.8652 (mtm) cc_final: 0.8392 (mtp) REVERT: B 323 GLU cc_start: 0.8888 (tp30) cc_final: 0.8193 (tp30) REVERT: C 250 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: C 323 GLU cc_start: 0.8893 (tp30) cc_final: 0.8153 (tp30) outliers start: 28 outliers final: 21 residues processed: 195 average time/residue: 0.1162 time to fit residues: 30.6619 Evaluate side-chains 197 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN C 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.099916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.065286 restraints weight = 20124.537| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.49 r_work: 0.2733 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10269 Z= 0.173 Angle : 0.598 8.667 14010 Z= 0.319 Chirality : 0.047 0.181 1653 Planarity : 0.003 0.027 1815 Dihedral : 4.945 18.652 1365 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.36 % Allowed : 11.52 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.25), residues: 1275 helix: -2.50 (0.79), residues: 36 sheet: -0.61 (0.24), residues: 462 loop : -0.17 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 193 TYR 0.016 0.002 TYR E 149 PHE 0.021 0.002 PHE F 301 TRP 0.016 0.003 TRP A 296 HIS 0.001 0.000 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00393 (10269) covalent geometry : angle 0.59807 (14010) hydrogen bonds : bond 0.03279 ( 258) hydrogen bonds : angle 6.53298 ( 630) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.8901 (pt0) cc_final: 0.8558 (pt0) REVERT: A 276 MET cc_start: 0.8532 (ttm) cc_final: 0.8321 (mtp) REVERT: A 323 GLU cc_start: 0.8971 (tp30) cc_final: 0.8766 (mm-30) REVERT: D 143 LEU cc_start: 0.8337 (pt) cc_final: 0.7965 (tp) REVERT: D 210 GLN cc_start: 0.8828 (mp10) cc_final: 0.8458 (mp10) REVERT: D 271 TYR cc_start: 0.7055 (m-80) cc_final: 0.6651 (m-80) REVERT: E 210 GLN cc_start: 0.8246 (mp10) cc_final: 0.7864 (mp10) REVERT: F 112 GLN cc_start: 0.8434 (pm20) cc_final: 0.8147 (pm20) REVERT: B 181 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8946 (t0) REVERT: B 250 GLU cc_start: 0.8917 (pt0) cc_final: 0.8695 (pt0) REVERT: B 323 GLU cc_start: 0.8886 (tp30) cc_final: 0.8111 (tp30) REVERT: C 250 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8516 (pt0) REVERT: C 276 MET cc_start: 0.8478 (mtp) cc_final: 0.8192 (mtm) REVERT: C 323 GLU cc_start: 0.8865 (tp30) cc_final: 0.8174 (tp30) outliers start: 27 outliers final: 20 residues processed: 187 average time/residue: 0.1099 time to fit residues: 27.7130 Evaluate side-chains 190 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 10.0000 chunk 54 optimal weight: 0.0270 chunk 104 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.101016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.066491 restraints weight = 20078.986| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.46 r_work: 0.2762 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10269 Z= 0.143 Angle : 0.585 8.191 14010 Z= 0.311 Chirality : 0.047 0.179 1653 Planarity : 0.003 0.028 1815 Dihedral : 4.778 17.801 1365 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.66 % Allowed : 11.95 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.25), residues: 1275 helix: -2.45 (0.80), residues: 36 sheet: -0.64 (0.24), residues: 468 loop : -0.10 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 193 TYR 0.015 0.002 TYR E 149 PHE 0.025 0.002 PHE F 301 TRP 0.015 0.002 TRP C 296 HIS 0.001 0.000 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00326 (10269) covalent geometry : angle 0.58509 (14010) hydrogen bonds : bond 0.03172 ( 258) hydrogen bonds : angle 6.45304 ( 630) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.8894 (pt0) cc_final: 0.8511 (pt0) REVERT: A 276 MET cc_start: 0.8514 (ttm) cc_final: 0.8274 (mtp) REVERT: A 279 GLN cc_start: 0.7730 (pm20) cc_final: 0.7316 (pm20) REVERT: D 143 LEU cc_start: 0.8367 (pt) cc_final: 0.7990 (tp) REVERT: D 210 GLN cc_start: 0.8833 (mp10) cc_final: 0.8467 (mp10) REVERT: D 271 TYR cc_start: 0.7106 (m-80) cc_final: 0.6809 (m-80) REVERT: E 210 GLN cc_start: 0.8295 (mp10) cc_final: 0.7890 (mp10) REVERT: F 112 GLN cc_start: 0.8421 (pm20) cc_final: 0.8138 (pm20) REVERT: B 181 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8930 (t0) REVERT: B 250 GLU cc_start: 0.8915 (pt0) cc_final: 0.8696 (pt0) REVERT: B 323 GLU cc_start: 0.8823 (tp30) cc_final: 0.8103 (tp30) REVERT: C 250 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8479 (pt0) REVERT: C 323 GLU cc_start: 0.8803 (tp30) cc_final: 0.8127 (tp30) outliers start: 19 outliers final: 16 residues processed: 182 average time/residue: 0.1066 time to fit residues: 26.8570 Evaluate side-chains 181 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 2 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.103005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.068575 restraints weight = 19897.060| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.48 r_work: 0.2798 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10269 Z= 0.118 Angle : 0.571 8.973 14010 Z= 0.304 Chirality : 0.046 0.177 1653 Planarity : 0.003 0.028 1815 Dihedral : 4.508 18.165 1365 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.31 % Allowed : 12.30 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.25), residues: 1275 helix: -2.40 (0.79), residues: 36 sheet: -0.57 (0.24), residues: 465 loop : -0.10 (0.25), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 193 TYR 0.012 0.001 TYR A 320 PHE 0.023 0.002 PHE F 301 TRP 0.013 0.002 TRP C 296 HIS 0.001 0.000 HIS F 183 Details of bonding type rmsd covalent geometry : bond 0.00266 (10269) covalent geometry : angle 0.57097 (14010) hydrogen bonds : bond 0.03014 ( 258) hydrogen bonds : angle 6.34859 ( 630) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.8883 (pt0) cc_final: 0.8422 (pt0) REVERT: A 279 GLN cc_start: 0.7631 (pm20) cc_final: 0.7174 (pm20) REVERT: A 291 ARG cc_start: 0.8534 (ttm-80) cc_final: 0.8276 (ttm-80) REVERT: D 112 GLN cc_start: 0.8501 (pm20) cc_final: 0.8229 (pm20) REVERT: D 143 LEU cc_start: 0.8358 (pt) cc_final: 0.8037 (tp) REVERT: D 210 GLN cc_start: 0.8881 (mp10) cc_final: 0.8533 (mp10) REVERT: D 238 ASN cc_start: 0.8562 (p0) cc_final: 0.8253 (m-40) REVERT: D 271 TYR cc_start: 0.7052 (m-80) cc_final: 0.6759 (m-80) REVERT: E 193 ARG cc_start: 0.7668 (tpp80) cc_final: 0.7300 (tpp80) REVERT: E 210 GLN cc_start: 0.8353 (mp10) cc_final: 0.7935 (mp10) REVERT: F 112 GLN cc_start: 0.8446 (pm20) cc_final: 0.8170 (pm20) REVERT: F 210 GLN cc_start: 0.8804 (mp10) cc_final: 0.8533 (mp10) REVERT: B 250 GLU cc_start: 0.8884 (pt0) cc_final: 0.8646 (pt0) REVERT: B 323 GLU cc_start: 0.8726 (tp30) cc_final: 0.8088 (tp30) REVERT: C 236 MET cc_start: 0.9401 (mmp) cc_final: 0.9171 (mmp) REVERT: C 250 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8474 (pt0) REVERT: C 276 MET cc_start: 0.8481 (mtm) cc_final: 0.8250 (mtp) REVERT: C 319 TYR cc_start: 0.8566 (m-80) cc_final: 0.8223 (m-80) REVERT: C 323 GLU cc_start: 0.8733 (tp30) cc_final: 0.8145 (tp30) outliers start: 15 outliers final: 11 residues processed: 187 average time/residue: 0.1124 time to fit residues: 28.5441 Evaluate side-chains 179 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 116 optimal weight: 0.0970 chunk 63 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 54 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.103741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.069577 restraints weight = 20063.074| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.47 r_work: 0.2817 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10269 Z= 0.110 Angle : 0.567 8.902 14010 Z= 0.300 Chirality : 0.045 0.177 1653 Planarity : 0.003 0.028 1815 Dihedral : 4.396 17.697 1365 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.13 % Allowed : 13.09 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.25), residues: 1275 helix: -2.32 (0.80), residues: 36 sheet: -0.53 (0.24), residues: 465 loop : -0.04 (0.25), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 193 TYR 0.012 0.001 TYR E 172 PHE 0.026 0.002 PHE D 301 TRP 0.013 0.002 TRP C 296 HIS 0.001 0.000 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00247 (10269) covalent geometry : angle 0.56724 (14010) hydrogen bonds : bond 0.03020 ( 258) hydrogen bonds : angle 6.29730 ( 630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2583.05 seconds wall clock time: 45 minutes 0.30 seconds (2700.30 seconds total)