Starting phenix.real_space_refine on Tue Sep 24 08:43:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/09_2024/6xjh_22210_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/09_2024/6xjh_22210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/09_2024/6xjh_22210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/09_2024/6xjh_22210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/09_2024/6xjh_22210_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/09_2024/6xjh_22210_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 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 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 5008 2.51 5 N 1210 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7596 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2030 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "C" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1736 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 1 Chain: "C" 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} Restraints were copied for chains: D, B Time building chain proxies: 5.14, per 1000 atoms: 0.68 Number of scatterers: 7596 At special positions: 0 Unit cell: (75.98, 100.87, 106.11, 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 36 16.00 P 6 15.00 Mg 2 11.99 O 1334 8.00 N 1210 7.00 C 5008 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: 1.91 Conformation dependent library (CDL) restraints added in 987.6 milliseconds 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 67.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid -4 through 15 Processing helix chain 'A' and resid 17 through 38 removed outlier: 3.705A pdb=" N TYR A 21 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 80 removed outlier: 3.562A pdb=" N VAL A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 89 through 126 Processing helix chain 'A' and resid 132 through 162 Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.574A pdb=" N VAL A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Proline residue: A 179 - end of helix Proline residue: A 183 - end of helix Processing helix chain 'A' and resid 191 through 200 removed outlier: 4.083A pdb=" N ASP A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 210 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 219 through 242 Processing helix chain 'B' and resid -3 through 15 Processing helix chain 'B' and resid 17 through 38 removed outlier: 3.705A pdb=" N TYR B 21 " --> pdb=" O SER B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 80 removed outlier: 3.563A pdb=" N VAL B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 86 Processing helix chain 'B' and resid 89 through 126 Processing helix chain 'B' and resid 132 through 162 Processing helix chain 'B' and resid 164 through 186 removed outlier: 3.575A pdb=" N VAL B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Proline residue: B 179 - end of helix Proline residue: B 183 - end of helix Processing helix chain 'B' and resid 191 through 200 removed outlier: 4.084A pdb=" N ASP B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 219 through 242 Processing helix chain 'C' and resid 38 through 48 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 96 through 108 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 121 through 135 Processing helix chain 'C' and resid 151 through 169 removed outlier: 4.068A pdb=" N ASN C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 277 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 96 through 108 Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 121 through 135 Processing helix chain 'D' and resid 151 through 169 removed outlier: 4.068A pdb=" N ASN D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 184 Processing helix chain 'D' and resid 277 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 21 removed outlier: 6.311A pdb=" N LYS C 8 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE C 6 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 19 " --> pdb=" O GLU C 4 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU C 4 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE C 21 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LYS C 2 " --> pdb=" O PHE C 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.437A pdb=" N LEU C 141 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER C 176 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU C 143 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE C 28 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL C 191 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY C 30 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU C 193 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 32 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN C 200 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG C 194 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N PHE C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 13 through 21 removed outlier: 6.310A pdb=" N LYS D 8 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE D 6 " --> pdb=" O ASN D 17 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE D 19 " --> pdb=" O GLU D 4 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU D 4 " --> pdb=" O ILE D 19 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE D 21 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS D 2 " --> pdb=" O PHE D 21 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.436A pdb=" N LEU D 141 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N SER D 176 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU D 143 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE D 28 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL D 191 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY D 30 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU D 193 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE D 32 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 200 " --> pdb=" O PHE D 192 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG D 194 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1389 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: 2.01 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1536 1.32 - 1.47: 2716 1.47 - 1.61: 3434 1.61 - 1.75: 16 1.75 - 1.90: 52 Bond restraints: 7754 Sorted by residual: bond pdb=" C VAL D 199 " pdb=" N GLN D 200 " ideal model delta sigma weight residual 1.330 1.513 -0.183 1.45e-02 4.76e+03 1.59e+02 bond pdb=" C VAL C 199 " pdb=" N GLN C 200 " ideal model delta sigma weight residual 1.330 1.512 -0.182 1.45e-02 4.76e+03 1.58e+02 bond pdb=" CB HIS B 115 " pdb=" CG HIS B 115 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.11e+01 bond pdb=" CB HIS A 115 " pdb=" CG HIS A 115 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.10e+01 bond pdb=" CB GLN B 222 " pdb=" CG GLN B 222 " ideal model delta sigma weight residual 1.520 1.360 0.160 3.00e-02 1.11e+03 2.83e+01 ... (remaining 7749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 9533 2.66 - 5.32: 828 5.32 - 7.98: 105 7.98 - 10.65: 10 10.65 - 13.31: 6 Bond angle restraints: 10482 Sorted by residual: angle pdb=" N ILE B 167 " pdb=" CA ILE B 167 " pdb=" C ILE B 167 " ideal model delta sigma weight residual 111.58 104.54 7.04 1.06e+00 8.90e-01 4.41e+01 angle pdb=" N ILE A 167 " pdb=" CA ILE A 167 " pdb=" C ILE A 167 " ideal model delta sigma weight residual 111.58 104.55 7.03 1.06e+00 8.90e-01 4.40e+01 angle pdb=" CA PHE A 55 " pdb=" CB PHE A 55 " pdb=" CG PHE A 55 " ideal model delta sigma weight residual 113.80 120.37 -6.57 1.00e+00 1.00e+00 4.32e+01 angle pdb=" CA PHE B 55 " pdb=" CB PHE B 55 " pdb=" CG PHE B 55 " ideal model delta sigma weight residual 113.80 120.34 -6.54 1.00e+00 1.00e+00 4.28e+01 angle pdb=" C VAL B -4 " pdb=" N PRO B -3 " pdb=" CA PRO B -3 " ideal model delta sigma weight residual 119.56 126.19 -6.63 1.02e+00 9.61e-01 4.23e+01 ... (remaining 10477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 4490 22.45 - 44.89: 100 44.89 - 67.34: 18 67.34 - 89.78: 10 89.78 - 112.23: 2 Dihedral angle restraints: 4620 sinusoidal: 1880 harmonic: 2740 Sorted by residual: dihedral pdb=" O1A AGS C 301 " pdb=" O3A AGS C 301 " pdb=" PA AGS C 301 " pdb=" PB AGS C 301 " ideal model delta sinusoidal sigma weight residual -67.73 44.50 -112.23 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" O1A AGS D 301 " pdb=" O3A AGS D 301 " pdb=" PA AGS D 301 " pdb=" PB AGS D 301 " ideal model delta sinusoidal sigma weight residual -67.73 44.46 -112.19 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C ILE B 188 " pdb=" N ILE B 188 " pdb=" CA ILE B 188 " pdb=" CB ILE B 188 " ideal model delta harmonic sigma weight residual -122.00 -130.51 8.51 0 2.50e+00 1.60e-01 1.16e+01 ... (remaining 4617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 673 0.067 - 0.134: 386 0.134 - 0.201: 124 0.201 - 0.268: 36 0.268 - 0.335: 11 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CB VAL D 166 " pdb=" CA VAL D 166 " pdb=" CG1 VAL D 166 " pdb=" CG2 VAL D 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB VAL C 166 " pdb=" CA VAL C 166 " pdb=" CG1 VAL C 166 " pdb=" CG2 VAL C 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA ARG D 189 " pdb=" N ARG D 189 " pdb=" C ARG D 189 " pdb=" CB ARG D 189 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1227 not shown) Planarity restraints: 1264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 206 " -0.069 2.00e-02 2.50e+03 3.63e-02 2.63e+01 pdb=" CG TYR B 206 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 206 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 206 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR B 206 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR B 206 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 206 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 206 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 206 " 0.068 2.00e-02 2.50e+03 3.61e-02 2.61e+01 pdb=" CG TYR A 206 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 206 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 206 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 206 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR A 206 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 206 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 206 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 199 " -0.019 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C VAL C 199 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL C 199 " -0.024 2.00e-02 2.50e+03 pdb=" N GLN C 200 " -0.019 2.00e-02 2.50e+03 ... (remaining 1261 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 799 2.72 - 3.26: 8129 3.26 - 3.81: 12766 3.81 - 4.35: 16198 4.35 - 4.90: 26334 Nonbonded interactions: 64226 Sorted by model distance: nonbonded pdb=" O2G AGS D 301 " pdb="MG MG D 302 " model vdw 2.173 2.170 nonbonded pdb=" O2G AGS C 301 " pdb="MG MG C 302 " model vdw 2.173 2.170 nonbonded pdb=" N LYS D 39 " pdb=" O1B AGS D 301 " model vdw 2.257 3.120 nonbonded pdb=" N LYS C 39 " pdb=" O1B AGS C 301 " model vdw 2.258 3.120 nonbonded pdb=" OG1 THR D 40 " pdb="MG MG D 302 " model vdw 2.272 2.170 ... (remaining 64221 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.260 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.620 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 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 : 0.019 0.183 7754 Z= 1.266 Angle : 1.641 13.306 10482 Z= 1.126 Chirality : 0.095 0.335 1230 Planarity : 0.008 0.036 1264 Dihedral : 11.428 112.230 2852 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.48 % Allowed : 0.95 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 928 helix: 1.29 (0.20), residues: 558 sheet: 1.10 (0.75), residues: 50 loop : -0.22 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.007 TRP A 223 HIS 0.007 0.002 HIS C 178 PHE 0.030 0.006 PHE B 55 TYR 0.069 0.008 TYR B 206 ARG 0.011 0.002 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 416 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 96 TYR cc_start: 0.8034 (t80) cc_final: 0.7750 (t80) REVERT: A 115 HIS cc_start: 0.8383 (t-90) cc_final: 0.8132 (t-170) REVERT: A 122 VAL cc_start: 0.8548 (t) cc_final: 0.7827 (t) REVERT: A 130 ASN cc_start: 0.6500 (m-40) cc_final: 0.5964 (m-40) REVERT: A 166 MET cc_start: 0.7154 (mmp) cc_final: 0.5945 (ptp) REVERT: A 206 TYR cc_start: 0.7317 (p90) cc_final: 0.7025 (p90) REVERT: A 209 ASP cc_start: 0.7685 (t70) cc_final: 0.7294 (m-30) REVERT: A 220 ASN cc_start: 0.8146 (m-40) cc_final: 0.7893 (m110) REVERT: A 223 TRP cc_start: 0.7890 (t-100) cc_final: 0.7351 (t60) REVERT: A 243 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7856 (mmtt) REVERT: B 42 MET cc_start: 0.4106 (tpt) cc_final: 0.3122 (ptt) REVERT: B 70 VAL cc_start: 0.8394 (t) cc_final: 0.8048 (p) REVERT: B 106 LEU cc_start: 0.8455 (mm) cc_final: 0.8242 (mt) REVERT: B 115 HIS cc_start: 0.8191 (t-90) cc_final: 0.7622 (t-170) REVERT: B 122 VAL cc_start: 0.8676 (t) cc_final: 0.8404 (t) REVERT: B 209 ASP cc_start: 0.8031 (t70) cc_final: 0.7517 (m-30) REVERT: B 211 MET cc_start: 0.8414 (mtp) cc_final: 0.8115 (mtm) REVERT: B 220 ASN cc_start: 0.8351 (m-40) cc_final: 0.8095 (m110) REVERT: B 221 TRP cc_start: 0.8291 (m100) cc_final: 0.7873 (m100) REVERT: B 243 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8027 (mmtt) REVERT: C 3 LEU cc_start: 0.8564 (mt) cc_final: 0.8234 (mt) REVERT: C 43 MET cc_start: 0.8383 (mtm) cc_final: 0.8042 (mtp) REVERT: C 49 ASN cc_start: 0.8163 (m110) cc_final: 0.7928 (m-40) REVERT: C 56 LYS cc_start: 0.7501 (tttt) cc_final: 0.7300 (tptt) REVERT: C 58 ASP cc_start: 0.7504 (t0) cc_final: 0.7233 (t70) REVERT: C 63 ASP cc_start: 0.6664 (m-30) cc_final: 0.6409 (p0) REVERT: C 71 HIS cc_start: 0.7468 (m-70) cc_final: 0.6291 (m-70) REVERT: C 91 LEU cc_start: 0.8556 (mt) cc_final: 0.8300 (mp) REVERT: C 99 TYR cc_start: 0.8282 (t80) cc_final: 0.7900 (t80) REVERT: C 157 ASP cc_start: 0.8631 (m-30) cc_final: 0.8243 (t0) REVERT: C 172 ARG cc_start: 0.7683 (mmt-90) cc_final: 0.7140 (mmm160) REVERT: C 179 LYS cc_start: 0.8589 (mttt) cc_final: 0.8244 (mtpt) REVERT: D 56 LYS cc_start: 0.7046 (tttt) cc_final: 0.6676 (tppt) REVERT: D 58 ASP cc_start: 0.7536 (t0) cc_final: 0.7330 (m-30) REVERT: D 75 TYR cc_start: 0.7969 (m-80) cc_final: 0.7756 (m-10) REVERT: D 91 LEU cc_start: 0.8503 (mt) cc_final: 0.8190 (mp) REVERT: D 99 TYR cc_start: 0.8610 (t80) cc_final: 0.8218 (t80) REVERT: D 124 MET cc_start: 0.8329 (mtt) cc_final: 0.7843 (mtm) REVERT: D 157 ASP cc_start: 0.8154 (m-30) cc_final: 0.7851 (t0) REVERT: D 165 LEU cc_start: 0.9043 (mt) cc_final: 0.8802 (mt) REVERT: D 179 LYS cc_start: 0.8586 (mttt) cc_final: 0.8144 (mttp) REVERT: D 183 ILE cc_start: 0.8217 (mt) cc_final: 0.7936 (mt) REVERT: D 185 LEU cc_start: 0.8686 (tp) cc_final: 0.8457 (tt) REVERT: D 194 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.7549 (ttp80) outliers start: 4 outliers final: 0 residues processed: 416 average time/residue: 0.1915 time to fit residues: 105.3880 Evaluate side-chains 237 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 178 HIS C 200 GLN ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 47 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7754 Z= 0.257 Angle : 0.707 7.424 10482 Z= 0.387 Chirality : 0.047 0.196 1230 Planarity : 0.004 0.033 1264 Dihedral : 10.228 120.937 1040 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.39 % Allowed : 11.40 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.27), residues: 928 helix: 2.29 (0.21), residues: 556 sheet: 0.75 (0.69), residues: 58 loop : -0.37 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 223 HIS 0.004 0.001 HIS B 47 PHE 0.019 0.002 PHE C 23 TYR 0.029 0.002 TYR B 206 ARG 0.005 0.001 ARG A -2 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 287 time to evaluate : 0.879 Fit side-chains REVERT: A 34 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7590 (mm-40) REVERT: A 141 TRP cc_start: 0.7965 (m100) cc_final: 0.7692 (m100) REVERT: A 166 MET cc_start: 0.6560 (mmp) cc_final: 0.5471 (ttm) REVERT: A 204 PHE cc_start: 0.7143 (m-80) cc_final: 0.6250 (m-80) REVERT: A 209 ASP cc_start: 0.7513 (t70) cc_final: 0.7232 (m-30) REVERT: A 220 ASN cc_start: 0.8489 (m-40) cc_final: 0.8274 (m110) REVERT: A 233 PHE cc_start: 0.8058 (m-80) cc_final: 0.7804 (m-80) REVERT: A 243 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7864 (mmtt) REVERT: B -2 ARG cc_start: 0.6315 (mtm-85) cc_final: 0.6010 (mmm160) REVERT: B 51 TYR cc_start: 0.7270 (m-80) cc_final: 0.7066 (m-10) REVERT: B 84 GLN cc_start: 0.8549 (tt0) cc_final: 0.8032 (tt0) REVERT: B 87 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7566 (mmm) REVERT: B 115 HIS cc_start: 0.7814 (t-90) cc_final: 0.7564 (t-170) REVERT: B 122 VAL cc_start: 0.8565 (t) cc_final: 0.8141 (t) REVERT: B 152 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8506 (mm) REVERT: B 209 ASP cc_start: 0.7572 (t70) cc_final: 0.7347 (m-30) REVERT: B 243 LYS cc_start: 0.8432 (mmtt) cc_final: 0.7953 (mmtt) REVERT: C 4 GLU cc_start: 0.7181 (mp0) cc_final: 0.6854 (mp0) REVERT: C 43 MET cc_start: 0.8078 (mtm) cc_final: 0.7807 (mtt) REVERT: C 49 ASN cc_start: 0.8198 (m110) cc_final: 0.7981 (m-40) REVERT: C 70 GLU cc_start: 0.7823 (tp30) cc_final: 0.7494 (tp30) REVERT: C 71 HIS cc_start: 0.7224 (m-70) cc_final: 0.6930 (m90) REVERT: C 99 TYR cc_start: 0.8140 (t80) cc_final: 0.7693 (t80) REVERT: C 157 ASP cc_start: 0.8586 (m-30) cc_final: 0.8332 (t70) REVERT: C 172 ARG cc_start: 0.7370 (mmt-90) cc_final: 0.7108 (mmm160) REVERT: C 181 GLU cc_start: 0.8479 (mp0) cc_final: 0.8134 (pm20) REVERT: C 194 ARG cc_start: 0.8062 (ttp-170) cc_final: 0.7697 (ttp80) REVERT: D 4 GLU cc_start: 0.7648 (mp0) cc_final: 0.7341 (mp0) REVERT: D 64 ASN cc_start: 0.7899 (m-40) cc_final: 0.7561 (m110) REVERT: D 157 ASP cc_start: 0.8075 (m-30) cc_final: 0.7829 (t0) REVERT: D 181 GLU cc_start: 0.8533 (mp0) cc_final: 0.7923 (pm20) REVERT: D 185 LEU cc_start: 0.8746 (tp) cc_final: 0.8501 (tt) REVERT: D 194 ARG cc_start: 0.7905 (ttp-170) cc_final: 0.7610 (ttp80) outliers start: 37 outliers final: 26 residues processed: 314 average time/residue: 0.1660 time to fit residues: 71.6237 Evaluate side-chains 258 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 230 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 276 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN B 220 ASN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 71 HIS D 285 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7754 Z= 0.237 Angle : 0.632 8.013 10482 Z= 0.341 Chirality : 0.045 0.188 1230 Planarity : 0.004 0.038 1264 Dihedral : 9.961 113.842 1040 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.34 % Allowed : 15.08 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 928 helix: 2.08 (0.21), residues: 560 sheet: 0.22 (0.70), residues: 58 loop : -0.84 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 60 HIS 0.002 0.001 HIS C 197 PHE 0.024 0.002 PHE A 111 TYR 0.045 0.002 TYR A 206 ARG 0.003 0.000 ARG D 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 248 time to evaluate : 0.890 Fit side-chains REVERT: A 141 TRP cc_start: 0.7875 (m100) cc_final: 0.7537 (m100) REVERT: A 166 MET cc_start: 0.6278 (mmp) cc_final: 0.5259 (ttm) REVERT: A 204 PHE cc_start: 0.7326 (m-80) cc_final: 0.6384 (m-80) REVERT: A 209 ASP cc_start: 0.7431 (t70) cc_final: 0.7160 (m-30) REVERT: A 220 ASN cc_start: 0.8472 (m-40) cc_final: 0.8245 (m110) REVERT: A 243 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7813 (mmtt) REVERT: B 84 GLN cc_start: 0.8505 (tt0) cc_final: 0.8212 (tt0) REVERT: B 87 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7555 (mmm) REVERT: B 115 HIS cc_start: 0.7761 (t-90) cc_final: 0.7523 (t-170) REVERT: B 152 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8520 (mm) REVERT: B 209 ASP cc_start: 0.7599 (t70) cc_final: 0.7330 (m-30) REVERT: B 243 LYS cc_start: 0.8432 (mmtt) cc_final: 0.7964 (mmtt) REVERT: C 3 LEU cc_start: 0.8404 (mt) cc_final: 0.7935 (mp) REVERT: C 4 GLU cc_start: 0.7048 (mp0) cc_final: 0.6701 (mp0) REVERT: C 43 MET cc_start: 0.8020 (mtm) cc_final: 0.7621 (mtt) REVERT: C 71 HIS cc_start: 0.7171 (m-70) cc_final: 0.6865 (m90) REVERT: C 99 TYR cc_start: 0.8227 (t80) cc_final: 0.7756 (t80) REVERT: C 157 ASP cc_start: 0.8629 (m-30) cc_final: 0.8339 (t70) REVERT: C 181 GLU cc_start: 0.8508 (mp0) cc_final: 0.8150 (pm20) REVERT: C 194 ARG cc_start: 0.8322 (ttp-170) cc_final: 0.7984 (ttp80) REVERT: C 200 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7190 (mt0) REVERT: D 4 GLU cc_start: 0.7673 (mp0) cc_final: 0.6941 (mp0) REVERT: D 64 ASN cc_start: 0.7884 (m-40) cc_final: 0.7541 (m110) REVERT: D 157 ASP cc_start: 0.8165 (m-30) cc_final: 0.7870 (t0) REVERT: D 181 GLU cc_start: 0.8329 (mp0) cc_final: 0.7866 (pm20) REVERT: D 194 ARG cc_start: 0.7928 (ttp-170) cc_final: 0.7509 (ttp80) outliers start: 45 outliers final: 34 residues processed: 272 average time/residue: 0.1612 time to fit residues: 61.1910 Evaluate side-chains 256 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 219 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 139 ASN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7754 Z= 0.209 Angle : 0.604 8.136 10482 Z= 0.326 Chirality : 0.045 0.367 1230 Planarity : 0.004 0.035 1264 Dihedral : 9.747 110.787 1040 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 5.23 % Allowed : 17.34 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.27), residues: 928 helix: 1.91 (0.21), residues: 562 sheet: 0.24 (0.71), residues: 58 loop : -1.04 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 60 HIS 0.002 0.000 HIS C 71 PHE 0.033 0.002 PHE B 143 TYR 0.040 0.002 TYR A 206 ARG 0.002 0.000 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 226 time to evaluate : 0.966 Fit side-chains REVERT: A 16 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7726 (mmtt) REVERT: A 141 TRP cc_start: 0.7884 (m100) cc_final: 0.7544 (m100) REVERT: A 166 MET cc_start: 0.6356 (mmp) cc_final: 0.5432 (ttm) REVERT: A 204 PHE cc_start: 0.7301 (m-80) cc_final: 0.6378 (m-80) REVERT: A 233 PHE cc_start: 0.8105 (m-80) cc_final: 0.7787 (m-80) REVERT: A 243 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7764 (mmtt) REVERT: B 11 LEU cc_start: 0.7978 (mt) cc_final: 0.7760 (tt) REVERT: B 84 GLN cc_start: 0.8518 (tt0) cc_final: 0.8043 (tp40) REVERT: B 87 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7531 (mmm) REVERT: B 139 ASN cc_start: 0.8342 (t0) cc_final: 0.7826 (t0) REVERT: B 152 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8496 (mm) REVERT: B 188 ILE cc_start: 0.5950 (mm) cc_final: 0.5718 (mt) REVERT: B 200 ASP cc_start: 0.8619 (m-30) cc_final: 0.7960 (t0) REVERT: B 209 ASP cc_start: 0.7527 (t70) cc_final: 0.7307 (m-30) REVERT: B 243 LYS cc_start: 0.8421 (mmtt) cc_final: 0.7991 (mmtt) REVERT: B 245 ASP cc_start: 0.5706 (m-30) cc_final: 0.5487 (m-30) REVERT: C 4 GLU cc_start: 0.7100 (mp0) cc_final: 0.6699 (mp0) REVERT: C 43 MET cc_start: 0.8158 (mtm) cc_final: 0.7841 (mtt) REVERT: C 70 GLU cc_start: 0.7910 (tp30) cc_final: 0.7704 (tp30) REVERT: C 71 HIS cc_start: 0.7141 (m-70) cc_final: 0.6843 (m90) REVERT: C 99 TYR cc_start: 0.8182 (t80) cc_final: 0.7734 (t80) REVERT: C 157 ASP cc_start: 0.8673 (m-30) cc_final: 0.8399 (t70) REVERT: C 181 GLU cc_start: 0.8586 (mp0) cc_final: 0.8294 (pm20) REVERT: D 3 LEU cc_start: 0.8638 (mt) cc_final: 0.8433 (mt) REVERT: D 4 GLU cc_start: 0.7642 (mp0) cc_final: 0.7287 (mp0) REVERT: D 157 ASP cc_start: 0.8226 (m-30) cc_final: 0.7952 (t0) REVERT: D 194 ARG cc_start: 0.7945 (ttp-170) cc_final: 0.7474 (ttp80) REVERT: D 285 ASN cc_start: 0.6578 (OUTLIER) cc_final: 0.6031 (t0) outliers start: 44 outliers final: 32 residues processed: 251 average time/residue: 0.1602 time to fit residues: 56.4524 Evaluate side-chains 255 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 220 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 75 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 0.0170 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 200 GLN ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 285 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7754 Z= 0.190 Angle : 0.594 7.814 10482 Z= 0.314 Chirality : 0.044 0.351 1230 Planarity : 0.003 0.034 1264 Dihedral : 9.517 108.506 1040 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.82 % Allowed : 17.46 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 928 helix: 1.80 (0.21), residues: 570 sheet: 0.18 (0.70), residues: 58 loop : -1.13 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 223 HIS 0.001 0.000 HIS B 115 PHE 0.018 0.001 PHE B 143 TYR 0.041 0.002 TYR A 206 ARG 0.002 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 232 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7967 (mmmt) cc_final: 0.7729 (mmtt) REVERT: A 141 TRP cc_start: 0.7903 (m100) cc_final: 0.7563 (m100) REVERT: A 166 MET cc_start: 0.6067 (mmp) cc_final: 0.5169 (ttm) REVERT: A 204 PHE cc_start: 0.7291 (m-80) cc_final: 0.6312 (m-80) REVERT: A 233 PHE cc_start: 0.8080 (m-80) cc_final: 0.7723 (m-80) REVERT: A 243 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7754 (mmtt) REVERT: B 84 GLN cc_start: 0.8499 (tt0) cc_final: 0.8067 (tp40) REVERT: B 87 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7626 (mmm) REVERT: B 152 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8495 (mm) REVERT: B 166 MET cc_start: 0.5504 (mmt) cc_final: 0.4645 (ttm) REVERT: B 188 ILE cc_start: 0.5895 (mm) cc_final: 0.5633 (mt) REVERT: B 200 ASP cc_start: 0.8525 (m-30) cc_final: 0.7926 (t0) REVERT: B 209 ASP cc_start: 0.7452 (t70) cc_final: 0.7244 (m-30) REVERT: B 243 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7960 (mmtt) REVERT: C 43 MET cc_start: 0.8125 (mtm) cc_final: 0.7851 (mtt) REVERT: C 70 GLU cc_start: 0.7863 (tp30) cc_final: 0.7614 (tp30) REVERT: C 71 HIS cc_start: 0.7131 (m-70) cc_final: 0.6922 (m90) REVERT: C 99 TYR cc_start: 0.8175 (t80) cc_final: 0.7800 (t80) REVERT: C 144 ASP cc_start: 0.8363 (t0) cc_final: 0.7828 (t0) REVERT: C 157 ASP cc_start: 0.8662 (m-30) cc_final: 0.8392 (t70) REVERT: C 181 GLU cc_start: 0.8629 (mp0) cc_final: 0.8360 (pm20) REVERT: C 202 VAL cc_start: 0.7679 (t) cc_final: 0.7438 (m) REVERT: C 204 MET cc_start: 0.6206 (pmm) cc_final: 0.6004 (pmm) REVERT: D 4 GLU cc_start: 0.7627 (mp0) cc_final: 0.7254 (mp0) REVERT: D 157 ASP cc_start: 0.8194 (m-30) cc_final: 0.7946 (t0) REVERT: D 194 ARG cc_start: 0.7975 (ttp-170) cc_final: 0.7477 (ttp80) REVERT: D 285 ASN cc_start: 0.6323 (OUTLIER) cc_final: 0.5810 (t0) outliers start: 49 outliers final: 33 residues processed: 257 average time/residue: 0.1630 time to fit residues: 58.7044 Evaluate side-chains 254 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 218 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 89 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 85 optimal weight: 5.9990 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 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7754 Z= 0.297 Angle : 0.645 8.316 10482 Z= 0.342 Chirality : 0.046 0.300 1230 Planarity : 0.004 0.036 1264 Dihedral : 9.553 103.797 1040 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 7.01 % Allowed : 16.63 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 928 helix: 1.74 (0.21), residues: 570 sheet: 0.04 (0.68), residues: 58 loop : -1.19 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 223 HIS 0.002 0.001 HIS C 197 PHE 0.019 0.002 PHE A 111 TYR 0.043 0.002 TYR A 206 ARG 0.004 0.001 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 221 time to evaluate : 0.934 Fit side-chains REVERT: A 6 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7449 (tt) REVERT: A 16 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7803 (mmtt) REVERT: A 141 TRP cc_start: 0.7953 (m100) cc_final: 0.7604 (m100) REVERT: A 166 MET cc_start: 0.6230 (mmp) cc_final: 0.5425 (ttm) REVERT: A 233 PHE cc_start: 0.8043 (m-80) cc_final: 0.7703 (m-80) REVERT: B 38 MET cc_start: 0.6772 (tpt) cc_final: 0.6475 (mmt) REVERT: B 84 GLN cc_start: 0.8557 (tt0) cc_final: 0.8141 (tp40) REVERT: B 87 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7895 (mmm) REVERT: B 115 HIS cc_start: 0.7764 (t-170) cc_final: 0.7551 (t-170) REVERT: B 116 TYR cc_start: 0.8333 (t80) cc_final: 0.8101 (t80) REVERT: B 152 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8593 (mm) REVERT: B 166 MET cc_start: 0.5646 (mmt) cc_final: 0.4683 (ttm) REVERT: B 188 ILE cc_start: 0.6067 (mm) cc_final: 0.5823 (mt) REVERT: B 209 ASP cc_start: 0.7530 (t70) cc_final: 0.7323 (m-30) REVERT: B 245 ASP cc_start: 0.5892 (m-30) cc_final: 0.5596 (m-30) REVERT: C 3 LEU cc_start: 0.8161 (mt) cc_final: 0.7934 (mt) REVERT: C 4 GLU cc_start: 0.7446 (mp0) cc_final: 0.6955 (mp0) REVERT: C 70 GLU cc_start: 0.7877 (tp30) cc_final: 0.7362 (tp30) REVERT: C 71 HIS cc_start: 0.7213 (m-70) cc_final: 0.6764 (m90) REVERT: C 99 TYR cc_start: 0.8285 (t80) cc_final: 0.8046 (t80) REVERT: C 126 GLN cc_start: 0.7433 (mt0) cc_final: 0.7225 (mt0) REVERT: C 157 ASP cc_start: 0.8700 (m-30) cc_final: 0.8422 (t70) REVERT: C 181 GLU cc_start: 0.8576 (mp0) cc_final: 0.8322 (pm20) REVERT: D 4 GLU cc_start: 0.7681 (mp0) cc_final: 0.7316 (mp0) REVERT: D 194 ARG cc_start: 0.8113 (ttp-170) cc_final: 0.7533 (ttp80) REVERT: D 285 ASN cc_start: 0.6269 (OUTLIER) cc_final: 0.5612 (t0) outliers start: 59 outliers final: 43 residues processed: 255 average time/residue: 0.1580 time to fit residues: 56.9100 Evaluate side-chains 259 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 212 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7754 Z= 0.220 Angle : 0.607 7.063 10482 Z= 0.325 Chirality : 0.044 0.254 1230 Planarity : 0.003 0.035 1264 Dihedral : 9.440 99.724 1040 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.58 % Allowed : 19.60 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 928 helix: 1.75 (0.21), residues: 564 sheet: -0.16 (0.68), residues: 58 loop : -1.29 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 223 HIS 0.002 0.001 HIS C 71 PHE 0.019 0.001 PHE A 111 TYR 0.046 0.002 TYR A 206 ARG 0.002 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 228 time to evaluate : 0.814 Fit side-chains REVERT: A 16 LYS cc_start: 0.8005 (mmmt) cc_final: 0.7790 (mmtt) REVERT: A 141 TRP cc_start: 0.7923 (m100) cc_final: 0.7589 (m100) REVERT: A 166 MET cc_start: 0.6021 (mmp) cc_final: 0.5157 (ttm) REVERT: A 233 PHE cc_start: 0.8066 (m-80) cc_final: 0.7734 (m-80) REVERT: B 15 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7323 (m-10) REVERT: B 84 GLN cc_start: 0.8552 (tt0) cc_final: 0.8147 (tp40) REVERT: B 87 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7779 (mmm) REVERT: B 116 TYR cc_start: 0.8262 (t80) cc_final: 0.8059 (t80) REVERT: B 152 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8599 (mm) REVERT: B 166 MET cc_start: 0.5633 (mmt) cc_final: 0.4652 (ttm) REVERT: B 188 ILE cc_start: 0.5988 (mm) cc_final: 0.5783 (mt) REVERT: C 1 MET cc_start: 0.6887 (tpp) cc_final: 0.6552 (tpt) REVERT: C 4 GLU cc_start: 0.7409 (mp0) cc_final: 0.6909 (mp0) REVERT: C 70 GLU cc_start: 0.7882 (tp30) cc_final: 0.7554 (tp30) REVERT: C 71 HIS cc_start: 0.7185 (m-70) cc_final: 0.6877 (m170) REVERT: C 99 TYR cc_start: 0.8294 (t80) cc_final: 0.8075 (t80) REVERT: C 157 ASP cc_start: 0.8641 (m-30) cc_final: 0.8374 (t70) REVERT: C 181 GLU cc_start: 0.8546 (mp0) cc_final: 0.8258 (pm20) REVERT: D 4 GLU cc_start: 0.7678 (mp0) cc_final: 0.7298 (mp0) REVERT: D 194 ARG cc_start: 0.8152 (ttp-170) cc_final: 0.7545 (ttp80) REVERT: D 285 ASN cc_start: 0.6527 (OUTLIER) cc_final: 0.5744 (t0) outliers start: 47 outliers final: 38 residues processed: 254 average time/residue: 0.1531 time to fit residues: 54.9642 Evaluate side-chains 258 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 216 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 0.0770 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 0.0370 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN B 123 GLN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 285 ASN D 35 ASN D 285 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7754 Z= 0.197 Angle : 0.607 8.126 10482 Z= 0.322 Chirality : 0.044 0.216 1230 Planarity : 0.003 0.035 1264 Dihedral : 9.301 98.656 1040 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.58 % Allowed : 20.55 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.27), residues: 928 helix: 1.70 (0.21), residues: 570 sheet: -0.11 (0.67), residues: 58 loop : -1.29 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 223 HIS 0.002 0.001 HIS B 115 PHE 0.018 0.001 PHE A 111 TYR 0.047 0.001 TYR A 206 ARG 0.002 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 229 time to evaluate : 0.874 Fit side-chains REVERT: A 16 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7792 (mmtt) REVERT: A 141 TRP cc_start: 0.7868 (m100) cc_final: 0.7559 (m100) REVERT: A 166 MET cc_start: 0.5980 (mmp) cc_final: 0.5134 (ttm) REVERT: B 15 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7329 (m-10) REVERT: B 60 TRP cc_start: 0.8346 (t60) cc_final: 0.7970 (t60) REVERT: B 84 GLN cc_start: 0.8538 (tt0) cc_final: 0.8154 (tp40) REVERT: B 87 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7766 (mmm) REVERT: B 152 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8498 (mm) REVERT: B 166 MET cc_start: 0.5615 (mmt) cc_final: 0.4542 (ttm) REVERT: B 188 ILE cc_start: 0.6053 (mm) cc_final: 0.5840 (mt) REVERT: C 3 LEU cc_start: 0.8177 (mt) cc_final: 0.7915 (mt) REVERT: C 4 GLU cc_start: 0.7393 (mp0) cc_final: 0.6882 (mp0) REVERT: C 70 GLU cc_start: 0.7848 (tp30) cc_final: 0.7563 (tp30) REVERT: C 71 HIS cc_start: 0.7193 (m-70) cc_final: 0.6929 (m170) REVERT: C 157 ASP cc_start: 0.8578 (m-30) cc_final: 0.8326 (t70) REVERT: C 181 GLU cc_start: 0.8522 (mp0) cc_final: 0.8296 (pm20) REVERT: D 4 GLU cc_start: 0.7666 (mp0) cc_final: 0.7285 (mp0) REVERT: D 124 MET cc_start: 0.7971 (mtm) cc_final: 0.7443 (mtm) REVERT: D 194 ARG cc_start: 0.8147 (ttp-170) cc_final: 0.7574 (ttp80) REVERT: D 285 ASN cc_start: 0.6275 (OUTLIER) cc_final: 0.5506 (t0) outliers start: 47 outliers final: 37 residues processed: 256 average time/residue: 0.1525 time to fit residues: 55.2880 Evaluate side-chains 262 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 221 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7754 Z= 0.204 Angle : 0.636 8.715 10482 Z= 0.333 Chirality : 0.045 0.199 1230 Planarity : 0.003 0.036 1264 Dihedral : 9.178 98.108 1040 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.11 % Allowed : 21.73 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.27), residues: 928 helix: 1.67 (0.21), residues: 570 sheet: -0.16 (0.68), residues: 58 loop : -1.35 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 223 HIS 0.002 0.001 HIS B 115 PHE 0.017 0.001 PHE A 111 TYR 0.047 0.002 TYR A 206 ARG 0.002 0.000 ARG D 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 230 time to evaluate : 0.849 Fit side-chains REVERT: A 141 TRP cc_start: 0.7873 (m100) cc_final: 0.7565 (m100) REVERT: A 166 MET cc_start: 0.6055 (mmp) cc_final: 0.5073 (ttm) REVERT: A 233 PHE cc_start: 0.7898 (m-80) cc_final: 0.7612 (m-80) REVERT: B 15 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7290 (m-10) REVERT: B 60 TRP cc_start: 0.8329 (t60) cc_final: 0.7950 (t60) REVERT: B 84 GLN cc_start: 0.8536 (tt0) cc_final: 0.8141 (tp40) REVERT: B 87 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7773 (mmm) REVERT: B 152 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8428 (mm) REVERT: B 166 MET cc_start: 0.5553 (mmt) cc_final: 0.4537 (ttm) REVERT: B 188 ILE cc_start: 0.5989 (mm) cc_final: 0.5777 (mt) REVERT: C 3 LEU cc_start: 0.8163 (mt) cc_final: 0.7897 (mt) REVERT: C 4 GLU cc_start: 0.7354 (mp0) cc_final: 0.6850 (mp0) REVERT: C 70 GLU cc_start: 0.7902 (tp30) cc_final: 0.7699 (tp30) REVERT: C 71 HIS cc_start: 0.7238 (m-70) cc_final: 0.7015 (m170) REVERT: C 157 ASP cc_start: 0.8455 (m-30) cc_final: 0.8238 (t70) REVERT: D 4 GLU cc_start: 0.7661 (mp0) cc_final: 0.7274 (mp0) REVERT: D 124 MET cc_start: 0.7897 (mtm) cc_final: 0.7419 (mtm) REVERT: D 194 ARG cc_start: 0.8135 (ttp-170) cc_final: 0.7615 (ttp80) REVERT: D 285 ASN cc_start: 0.6273 (OUTLIER) cc_final: 0.5621 (t0) outliers start: 43 outliers final: 35 residues processed: 257 average time/residue: 0.1520 time to fit residues: 55.6758 Evaluate side-chains 259 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 220 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 84 optimal weight: 0.3980 chunk 72 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7754 Z= 0.226 Angle : 0.655 11.307 10482 Z= 0.341 Chirality : 0.044 0.197 1230 Planarity : 0.003 0.036 1264 Dihedral : 9.119 97.063 1040 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.23 % Allowed : 21.38 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.27), residues: 928 helix: 1.68 (0.21), residues: 570 sheet: -0.00 (0.71), residues: 58 loop : -1.40 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 223 HIS 0.002 0.001 HIS B 115 PHE 0.031 0.001 PHE B 218 TYR 0.044 0.002 TYR A 206 ARG 0.002 0.000 ARG C 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 221 time to evaluate : 0.928 Fit side-chains REVERT: A 141 TRP cc_start: 0.7886 (m100) cc_final: 0.7586 (m100) REVERT: A 166 MET cc_start: 0.6286 (mmp) cc_final: 0.5226 (ttm) REVERT: A 233 PHE cc_start: 0.7866 (m-80) cc_final: 0.7594 (m-80) REVERT: B 15 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7308 (m-10) REVERT: B 60 TRP cc_start: 0.8335 (t60) cc_final: 0.7939 (t60) REVERT: B 84 GLN cc_start: 0.8549 (tt0) cc_final: 0.8151 (tp40) REVERT: B 87 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7840 (mmm) REVERT: B 152 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8582 (mm) REVERT: B 166 MET cc_start: 0.5574 (mmt) cc_final: 0.4463 (ttm) REVERT: B 188 ILE cc_start: 0.6000 (mm) cc_final: 0.5782 (mt) REVERT: C 4 GLU cc_start: 0.7421 (mp0) cc_final: 0.6984 (mp0) REVERT: C 70 GLU cc_start: 0.7882 (tp30) cc_final: 0.7590 (tp30) REVERT: C 71 HIS cc_start: 0.7203 (m-70) cc_final: 0.6725 (m170) REVERT: D 124 MET cc_start: 0.7714 (mtm) cc_final: 0.7283 (mtm) REVERT: D 194 ARG cc_start: 0.8204 (ttp-170) cc_final: 0.7705 (ttp80) REVERT: D 285 ASN cc_start: 0.5785 (OUTLIER) cc_final: 0.5215 (t0) outliers start: 44 outliers final: 37 residues processed: 247 average time/residue: 0.1548 time to fit residues: 54.2191 Evaluate side-chains 256 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 215 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 285 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 64 optimal weight: 0.0980 chunk 4 optimal weight: 0.0570 chunk 52 optimal weight: 0.8980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.092680 restraints weight = 13991.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095803 restraints weight = 7056.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098172 restraints weight = 4622.359| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7754 Z= 0.194 Angle : 0.644 9.685 10482 Z= 0.333 Chirality : 0.044 0.192 1230 Planarity : 0.003 0.035 1264 Dihedral : 8.928 96.805 1040 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.39 % Allowed : 22.80 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.27), residues: 928 helix: 1.72 (0.21), residues: 570 sheet: 0.08 (0.73), residues: 58 loop : -1.44 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 223 HIS 0.002 0.001 HIS B 115 PHE 0.029 0.001 PHE B 218 TYR 0.045 0.001 TYR A 206 ARG 0.004 0.000 ARG D 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1872.49 seconds wall clock time: 34 minutes 3.83 seconds (2043.83 seconds total)