Starting phenix.real_space_refine on Wed Sep 17 11:14:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xql_38580/09_2025/8xql_38580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xql_38580/09_2025/8xql_38580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xql_38580/09_2025/8xql_38580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xql_38580/09_2025/8xql_38580.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xql_38580/09_2025/8xql_38580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xql_38580/09_2025/8xql_38580.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5342 2.51 5 N 1439 2.21 5 O 1539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8368 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1964 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 981 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2293 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain breaks: 1 Chain: "R" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'CLR': 1, 'GOQ': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.20, per 1000 atoms: 0.26 Number of scatterers: 8368 At special positions: 0 Unit cell: (75.92, 99.84, 133.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1539 8.00 N 1439 7.00 C 5342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS N 100 " - pdb=" SG CYS N 108 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 488.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 45.2% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.804A pdb=" N ASN A 104 " --> pdb=" O GLN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 135 through 138 removed outlier: 3.728A pdb=" N ARG A 138 " --> pdb=" O ARG A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.529A pdb=" N ALA A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.529A pdb=" N TYR A 173 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 206 Processing helix chain 'A' and resid 222 through 246 removed outlier: 3.781A pdb=" N ASN A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.508A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.643A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'N' and resid 29 through 33 removed outlier: 3.570A pdb=" N ASN N 32 " --> pdb=" O THR N 29 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR N 33 " --> pdb=" O PHE N 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 29 through 33' Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'R' and resid 3 through 37 Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 74 through 78 Processing helix chain 'R' and resid 80 through 112 Processing helix chain 'R' and resid 116 through 124 removed outlier: 3.646A pdb=" N TRP R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 158 removed outlier: 4.591A pdb=" N VAL R 139 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 216 Proline residue: R 190 - end of helix Processing helix chain 'R' and resid 220 through 254 Processing helix chain 'R' and resid 260 through 284 removed outlier: 3.822A pdb=" N LEU R 264 " --> pdb=" O ASN R 260 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR R 272 " --> pdb=" O MET R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.914A pdb=" N SER R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 79 removed outlier: 6.120A pdb=" N HIS A 37 " --> pdb=" O HIS A 85 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 87 " --> pdb=" O HIS A 37 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A 39 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 109 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE A 145 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE A 111 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 142 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N HIS A 217 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A 144 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 52 removed outlier: 5.491A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.867A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.058A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.862A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.292A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.410A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.610A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 8 Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 61 removed outlier: 6.448A pdb=" N TRP N 37 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP N 51 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET N 35 " --> pdb=" O ASP N 51 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2687 1.34 - 1.46: 1477 1.46 - 1.57: 4312 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 8545 Sorted by residual: bond pdb=" C8 GOQ R 502 " pdb=" C9 GOQ R 502 " ideal model delta sigma weight residual 1.350 1.388 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C5 GOQ R 502 " pdb=" C6 GOQ R 502 " ideal model delta sigma weight residual 1.454 1.417 0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" C5 GOQ R 501 " pdb=" C6 GOQ R 501 " ideal model delta sigma weight residual 1.454 1.420 0.034 2.00e-02 2.50e+03 2.83e+00 bond pdb=" C8 GOQ R 501 " pdb=" C9 GOQ R 501 " ideal model delta sigma weight residual 1.350 1.383 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C10 GOQ R 501 " pdb=" C9 GOQ R 501 " ideal model delta sigma weight residual 1.423 1.392 0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 8540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11359 2.00 - 4.00: 180 4.00 - 6.00: 29 6.00 - 8.00: 3 8.00 - 10.00: 1 Bond angle restraints: 11572 Sorted by residual: angle pdb=" CA VAL N 127 " pdb=" CB VAL N 127 " pdb=" CG1 VAL N 127 " ideal model delta sigma weight residual 110.40 115.55 -5.15 1.70e+00 3.46e-01 9.19e+00 angle pdb=" C CYS N 100 " pdb=" CA CYS N 100 " pdb=" CB CYS N 100 " ideal model delta sigma weight residual 109.11 113.50 -4.39 1.50e+00 4.44e-01 8.57e+00 angle pdb=" CA LEU A 157 " pdb=" CB LEU A 157 " pdb=" CG LEU A 157 " ideal model delta sigma weight residual 116.30 126.30 -10.00 3.50e+00 8.16e-02 8.17e+00 angle pdb=" N PRO N 101 " pdb=" CA PRO N 101 " pdb=" C PRO N 101 " ideal model delta sigma weight residual 112.47 118.21 -5.74 2.06e+00 2.36e-01 7.77e+00 angle pdb=" C PHE R 72 " pdb=" CA PHE R 72 " pdb=" CB PHE R 72 " ideal model delta sigma weight residual 110.17 115.58 -5.41 1.97e+00 2.58e-01 7.54e+00 ... (remaining 11567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4469 17.86 - 35.71: 487 35.71 - 53.57: 120 53.57 - 71.42: 11 71.42 - 89.28: 7 Dihedral angle restraints: 5094 sinusoidal: 2052 harmonic: 3042 Sorted by residual: dihedral pdb=" CA CYS N 100 " pdb=" C CYS N 100 " pdb=" N PRO N 101 " pdb=" CA PRO N 101 " ideal model delta harmonic sigma weight residual -180.00 -151.65 -28.35 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 97 " pdb=" CB CYS N 97 " ideal model delta sinusoidal sigma weight residual 93.00 57.60 35.40 1 1.00e+01 1.00e-02 1.77e+01 dihedral pdb=" CA CYS N 108 " pdb=" C CYS N 108 " pdb=" N PHE N 109 " pdb=" CA PHE N 109 " ideal model delta harmonic sigma weight residual 180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 5091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 817 0.034 - 0.068: 342 0.068 - 0.101: 103 0.101 - 0.135: 38 0.135 - 0.169: 7 Chirality restraints: 1307 Sorted by residual: chirality pdb=" CA PRO N 101 " pdb=" N PRO N 101 " pdb=" C PRO N 101 " pdb=" CB PRO N 101 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB ILE R 19 " pdb=" CA ILE R 19 " pdb=" CG1 ILE R 19 " pdb=" CG2 ILE R 19 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CB ILE R 242 " pdb=" CA ILE R 242 " pdb=" CG1 ILE R 242 " pdb=" CG2 ILE R 242 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 1304 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 87 " -0.006 2.00e-02 2.50e+03 1.13e-02 2.24e+00 pdb=" CG PHE A 87 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 87 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 87 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 87 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 87 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 87 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO C 49 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 134 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.02e+00 pdb=" CG ASN A 134 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 134 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 134 " -0.008 2.00e-02 2.50e+03 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 297 2.70 - 3.25: 8606 3.25 - 3.80: 14406 3.80 - 4.35: 17832 4.35 - 4.90: 29868 Nonbonded interactions: 71009 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.156 3.040 nonbonded pdb=" OD1 ASN R 24 " pdb=" OG SER R 277 " model vdw 2.188 3.040 nonbonded pdb=" O ALA A 44 " pdb=" OG SER A 47 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.221 3.040 ... (remaining 71004 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 0.005 0.057 8547 Z= 0.228 Angle : 0.631 10.001 11576 Z= 0.331 Chirality : 0.044 0.169 1307 Planarity : 0.004 0.038 1450 Dihedral : 15.562 89.276 3118 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 26.71 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.26), residues: 1038 helix: 2.36 (0.24), residues: 440 sheet: -0.24 (0.35), residues: 218 loop : -0.85 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.016 0.002 TYR N 96 PHE 0.023 0.002 PHE A 87 TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS R 151 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 8545) covalent geometry : angle 0.62783 (11572) SS BOND : bond 0.00485 ( 2) SS BOND : angle 3.38034 ( 4) hydrogen bonds : bond 0.12292 ( 480) hydrogen bonds : angle 5.26977 ( 1374) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 ASN cc_start: 0.8143 (m-40) cc_final: 0.7912 (m110) REVERT: B 186 ASP cc_start: 0.7639 (m-30) cc_final: 0.7428 (m-30) REVERT: B 226 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7636 (mt-10) outliers start: 0 outliers final: 1 residues processed: 224 average time/residue: 0.6053 time to fit residues: 143.6523 Evaluate side-chains 220 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.0050 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 155 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.134900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119241 restraints weight = 12104.309| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.05 r_work: 0.3402 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8547 Z= 0.189 Angle : 0.576 7.925 11576 Z= 0.304 Chirality : 0.042 0.180 1307 Planarity : 0.004 0.052 1450 Dihedral : 4.493 34.421 1213 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.14 % Favored : 95.66 % Rotamer: Outliers : 4.75 % Allowed : 22.30 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.26), residues: 1038 helix: 2.51 (0.23), residues: 440 sheet: -0.06 (0.36), residues: 210 loop : -0.84 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 97 TYR 0.015 0.001 TYR N 96 PHE 0.019 0.002 PHE A 87 TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 8545) covalent geometry : angle 0.57298 (11572) SS BOND : bond 0.00402 ( 2) SS BOND : angle 3.18853 ( 4) hydrogen bonds : bond 0.04544 ( 480) hydrogen bonds : angle 4.48090 ( 1374) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7477 (mtm-85) REVERT: A 134 ASN cc_start: 0.7525 (m-40) cc_final: 0.7179 (m-40) REVERT: B 100 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8135 (p) REVERT: B 119 ASN cc_start: 0.8359 (m-40) cc_final: 0.8126 (m110) REVERT: B 186 ASP cc_start: 0.7680 (m-30) cc_final: 0.7402 (m-30) REVERT: B 212 ASP cc_start: 0.7967 (t0) cc_final: 0.7699 (t0) REVERT: B 258 ASP cc_start: 0.8111 (t0) cc_final: 0.7625 (t0) REVERT: B 314 ARG cc_start: 0.8217 (ptm160) cc_final: 0.7928 (ptm160) REVERT: R 17 PHE cc_start: 0.8347 (t80) cc_final: 0.7978 (t80) REVERT: R 72 PHE cc_start: 0.7559 (t80) cc_final: 0.7331 (t80) REVERT: R 120 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7917 (mm) outliers start: 43 outliers final: 15 residues processed: 243 average time/residue: 0.5996 time to fit residues: 154.5726 Evaluate side-chains 239 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 221 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 235 THR Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 58 optimal weight: 0.0870 chunk 67 optimal weight: 0.0770 chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 126 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 75 GLN B 155 ASN B 176 GLN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.136550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120716 restraints weight = 11980.408| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.05 r_work: 0.3428 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8547 Z= 0.132 Angle : 0.529 7.241 11576 Z= 0.280 Chirality : 0.040 0.189 1307 Planarity : 0.004 0.036 1450 Dihedral : 4.309 34.913 1211 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.47 % Favored : 96.34 % Rotamer: Outliers : 3.64 % Allowed : 23.73 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.27), residues: 1038 helix: 2.71 (0.23), residues: 439 sheet: -0.00 (0.35), residues: 217 loop : -0.87 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.011 0.001 TYR N 96 PHE 0.019 0.002 PHE R 82 TRP 0.014 0.002 TRP B 99 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8545) covalent geometry : angle 0.52626 (11572) SS BOND : bond 0.00194 ( 2) SS BOND : angle 3.10683 ( 4) hydrogen bonds : bond 0.04052 ( 480) hydrogen bonds : angle 4.29174 ( 1374) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7389 (mtm-85) REVERT: A 202 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7708 (ttp-110) REVERT: B 46 ARG cc_start: 0.8483 (mtt-85) cc_final: 0.8237 (mtp-110) REVERT: B 137 ARG cc_start: 0.7886 (mmt-90) cc_final: 0.7531 (tpt170) REVERT: B 176 GLN cc_start: 0.8561 (mt0) cc_final: 0.8354 (mt0) REVERT: B 186 ASP cc_start: 0.7570 (m-30) cc_final: 0.7294 (m-30) REVERT: B 258 ASP cc_start: 0.8075 (t0) cc_final: 0.7476 (t0) REVERT: B 283 ARG cc_start: 0.8449 (tpt-90) cc_final: 0.8217 (tpt90) REVERT: B 314 ARG cc_start: 0.8073 (ptm160) cc_final: 0.7825 (ptm160) REVERT: R 17 PHE cc_start: 0.8438 (t80) cc_final: 0.7928 (t80) REVERT: R 72 PHE cc_start: 0.7502 (t80) cc_final: 0.7186 (t80) REVERT: R 120 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7855 (mm) outliers start: 33 outliers final: 14 residues processed: 232 average time/residue: 0.6183 time to fit residues: 151.9745 Evaluate side-chains 237 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.0040 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 75 GLN B 88 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.135877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120061 restraints weight = 12166.416| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.08 r_work: 0.3412 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8547 Z= 0.151 Angle : 0.543 7.716 11576 Z= 0.283 Chirality : 0.041 0.182 1307 Planarity : 0.004 0.038 1450 Dihedral : 4.289 34.750 1211 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.05 % Rotamer: Outliers : 3.53 % Allowed : 24.39 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.26), residues: 1038 helix: 2.70 (0.23), residues: 440 sheet: 0.06 (0.36), residues: 216 loop : -0.88 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.013 0.001 TYR N 96 PHE 0.022 0.002 PHE R 82 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8545) covalent geometry : angle 0.54002 (11572) SS BOND : bond 0.00444 ( 2) SS BOND : angle 2.90919 ( 4) hydrogen bonds : bond 0.04073 ( 480) hydrogen bonds : angle 4.25390 ( 1374) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7431 (mtm-85) REVERT: B 137 ARG cc_start: 0.7880 (mmt-90) cc_final: 0.7531 (tpt170) REVERT: B 186 ASP cc_start: 0.7656 (m-30) cc_final: 0.7300 (m-30) REVERT: B 237 ASN cc_start: 0.8496 (t0) cc_final: 0.8282 (t0) REVERT: B 258 ASP cc_start: 0.8075 (t0) cc_final: 0.7465 (t0) REVERT: B 283 ARG cc_start: 0.8484 (tpt-90) cc_final: 0.8227 (tpt90) REVERT: R 17 PHE cc_start: 0.8492 (t80) cc_final: 0.7878 (t80) REVERT: R 72 PHE cc_start: 0.7490 (t80) cc_final: 0.7139 (t80) REVERT: R 99 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8076 (tp) REVERT: R 120 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7828 (mm) outliers start: 32 outliers final: 13 residues processed: 243 average time/residue: 0.5978 time to fit residues: 153.8760 Evaluate side-chains 238 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 90 optimal weight: 2.9990 chunk 39 optimal weight: 0.0270 chunk 4 optimal weight: 0.4980 chunk 68 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 126 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 88 ASN B 119 ASN B 155 ASN B 176 GLN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.134856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118845 restraints weight = 12290.242| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.06 r_work: 0.3404 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8547 Z= 0.149 Angle : 0.547 8.418 11576 Z= 0.285 Chirality : 0.041 0.187 1307 Planarity : 0.003 0.038 1450 Dihedral : 4.303 34.812 1211 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.05 % Rotamer: Outliers : 3.53 % Allowed : 25.61 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.26), residues: 1038 helix: 2.75 (0.23), residues: 439 sheet: 0.22 (0.37), residues: 208 loop : -0.87 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 138 TYR 0.012 0.001 TYR N 96 PHE 0.022 0.001 PHE R 82 TRP 0.015 0.002 TRP R 60 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8545) covalent geometry : angle 0.54422 (11572) SS BOND : bond 0.00441 ( 2) SS BOND : angle 3.11522 ( 4) hydrogen bonds : bond 0.04043 ( 480) hydrogen bonds : angle 4.24111 ( 1374) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7472 (mtm-85) REVERT: A 182 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7441 (mm-30) REVERT: A 188 ARG cc_start: 0.7662 (pmm-80) cc_final: 0.7437 (mpp80) REVERT: B 119 ASN cc_start: 0.8107 (m-40) cc_final: 0.7902 (m110) REVERT: B 137 ARG cc_start: 0.7879 (mmt-90) cc_final: 0.7555 (tpt170) REVERT: B 186 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: B 239 ASN cc_start: 0.8219 (m110) cc_final: 0.7844 (m110) REVERT: B 258 ASP cc_start: 0.8096 (t0) cc_final: 0.7420 (t0) REVERT: B 314 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7812 (ptm160) REVERT: B 340 ASN cc_start: 0.7899 (t0) cc_final: 0.7650 (t0) REVERT: R 17 PHE cc_start: 0.8393 (t80) cc_final: 0.8056 (t80) REVERT: R 58 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7913 (tp) REVERT: R 72 PHE cc_start: 0.7437 (t80) cc_final: 0.7052 (t80) REVERT: R 99 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8090 (tp) REVERT: R 120 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7863 (mm) outliers start: 32 outliers final: 15 residues processed: 243 average time/residue: 0.6013 time to fit residues: 155.0322 Evaluate side-chains 245 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 82 optimal weight: 0.0060 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 126 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 88 ASN B 155 ASN B 237 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.135304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119335 restraints weight = 12190.763| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.05 r_work: 0.3409 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8547 Z= 0.135 Angle : 0.547 8.287 11576 Z= 0.284 Chirality : 0.041 0.185 1307 Planarity : 0.004 0.056 1450 Dihedral : 4.249 34.774 1211 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.15 % Rotamer: Outliers : 3.64 % Allowed : 25.83 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.27), residues: 1038 helix: 2.80 (0.23), residues: 439 sheet: 0.08 (0.36), residues: 222 loop : -0.85 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 138 TYR 0.012 0.001 TYR B 124 PHE 0.023 0.001 PHE R 82 TRP 0.016 0.001 TRP B 99 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8545) covalent geometry : angle 0.54469 (11572) SS BOND : bond 0.00505 ( 2) SS BOND : angle 2.73217 ( 4) hydrogen bonds : bond 0.03894 ( 480) hydrogen bonds : angle 4.21774 ( 1374) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7451 (mtm-85) REVERT: A 182 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7400 (mm-30) REVERT: B 42 ARG cc_start: 0.7558 (ttp80) cc_final: 0.7277 (ttp80) REVERT: B 125 ASN cc_start: 0.8351 (t0) cc_final: 0.8150 (t0) REVERT: B 186 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7243 (m-30) REVERT: B 237 ASN cc_start: 0.8470 (t0) cc_final: 0.8204 (t160) REVERT: B 239 ASN cc_start: 0.8219 (m110) cc_final: 0.7853 (m110) REVERT: B 258 ASP cc_start: 0.8059 (t0) cc_final: 0.7372 (t0) REVERT: R 17 PHE cc_start: 0.8422 (t80) cc_final: 0.8078 (t80) REVERT: R 58 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7925 (tp) REVERT: R 72 PHE cc_start: 0.7403 (t80) cc_final: 0.7031 (t80) REVERT: R 99 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8091 (tp) REVERT: R 120 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7825 (mm) outliers start: 33 outliers final: 15 residues processed: 239 average time/residue: 0.5739 time to fit residues: 145.8658 Evaluate side-chains 237 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 84 MET Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 40 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 88 ASN B 119 ASN B 142 HIS B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118634 restraints weight = 12058.013| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.05 r_work: 0.3391 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8547 Z= 0.197 Angle : 0.589 9.062 11576 Z= 0.307 Chirality : 0.043 0.183 1307 Planarity : 0.004 0.047 1450 Dihedral : 4.410 34.972 1211 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.66 % Rotamer: Outliers : 3.53 % Allowed : 26.27 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.26), residues: 1038 helix: 2.64 (0.23), residues: 439 sheet: 0.12 (0.37), residues: 202 loop : -0.95 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 49 TYR 0.015 0.001 TYR N 96 PHE 0.027 0.002 PHE A 87 TRP 0.017 0.002 TRP B 99 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8545) covalent geometry : angle 0.58633 (11572) SS BOND : bond 0.00543 ( 2) SS BOND : angle 3.10162 ( 4) hydrogen bonds : bond 0.04305 ( 480) hydrogen bonds : angle 4.34670 ( 1374) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7456 (mtm-85) REVERT: A 182 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7406 (mm-30) REVERT: A 188 ARG cc_start: 0.7691 (pmm-80) cc_final: 0.7415 (mpp80) REVERT: A 203 ILE cc_start: 0.8415 (mt) cc_final: 0.8164 (mp) REVERT: A 211 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7311 (mtm-85) REVERT: A 236 ASP cc_start: 0.8742 (t70) cc_final: 0.8430 (t70) REVERT: B 42 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7258 (ttp80) REVERT: B 119 ASN cc_start: 0.8249 (m-40) cc_final: 0.7979 (m110) REVERT: B 186 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7389 (m-30) REVERT: B 258 ASP cc_start: 0.8085 (t0) cc_final: 0.7417 (t0) REVERT: R 58 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7974 (tp) REVERT: R 72 PHE cc_start: 0.7414 (t80) cc_final: 0.7038 (t80) REVERT: R 120 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7864 (mm) outliers start: 32 outliers final: 15 residues processed: 238 average time/residue: 0.5878 time to fit residues: 148.5537 Evaluate side-chains 225 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.0470 chunk 81 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 17 optimal weight: 0.0060 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 overall best weight: 0.4294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 75 GLN B 88 ASN B 155 ASN B 237 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.135730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120036 restraints weight = 11937.846| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.05 r_work: 0.3425 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8547 Z= 0.144 Angle : 0.571 7.783 11576 Z= 0.299 Chirality : 0.042 0.181 1307 Planarity : 0.004 0.038 1450 Dihedral : 4.313 35.095 1211 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 2.54 % Allowed : 27.92 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.26), residues: 1038 helix: 2.74 (0.23), residues: 439 sheet: 0.12 (0.37), residues: 202 loop : -0.97 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.012 0.001 TYR B 124 PHE 0.038 0.002 PHE R 17 TRP 0.017 0.002 TRP B 99 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8545) covalent geometry : angle 0.56951 (11572) SS BOND : bond 0.00468 ( 2) SS BOND : angle 2.59145 ( 4) hydrogen bonds : bond 0.04034 ( 480) hydrogen bonds : angle 4.30535 ( 1374) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7447 (mtm-85) REVERT: A 182 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 188 ARG cc_start: 0.7658 (pmm-80) cc_final: 0.7394 (mpp80) REVERT: A 203 ILE cc_start: 0.8357 (mt) cc_final: 0.8114 (mp) REVERT: A 211 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7305 (mtm-85) REVERT: A 213 TYR cc_start: 0.8672 (m-80) cc_final: 0.8317 (m-80) REVERT: A 236 ASP cc_start: 0.8787 (t70) cc_final: 0.8467 (t0) REVERT: B 119 ASN cc_start: 0.8197 (m-40) cc_final: 0.7972 (m110) REVERT: B 186 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: B 237 ASN cc_start: 0.8515 (t0) cc_final: 0.8264 (t160) REVERT: B 239 ASN cc_start: 0.8203 (m110) cc_final: 0.7816 (m110) REVERT: B 258 ASP cc_start: 0.8057 (t0) cc_final: 0.7380 (t0) REVERT: R 58 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7934 (tp) REVERT: R 72 PHE cc_start: 0.7355 (t80) cc_final: 0.7003 (t80) REVERT: R 120 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7827 (mm) outliers start: 23 outliers final: 16 residues processed: 243 average time/residue: 0.5771 time to fit residues: 149.0982 Evaluate side-chains 254 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 41 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 0.0040 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 75 GLN B 142 HIS B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.135606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119936 restraints weight = 12049.717| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.05 r_work: 0.3414 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8547 Z= 0.164 Angle : 0.592 7.965 11576 Z= 0.309 Chirality : 0.043 0.183 1307 Planarity : 0.004 0.038 1450 Dihedral : 4.388 35.067 1211 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.05 % Rotamer: Outliers : 2.87 % Allowed : 28.15 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.26), residues: 1038 helix: 2.68 (0.23), residues: 439 sheet: 0.06 (0.37), residues: 202 loop : -1.00 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 138 TYR 0.013 0.001 TYR B 124 PHE 0.038 0.002 PHE R 17 TRP 0.018 0.002 TRP B 99 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8545) covalent geometry : angle 0.58966 (11572) SS BOND : bond 0.00414 ( 2) SS BOND : angle 2.65117 ( 4) hydrogen bonds : bond 0.04148 ( 480) hydrogen bonds : angle 4.35276 ( 1374) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7510 (mtm-85) REVERT: A 182 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7357 (mm-30) REVERT: A 188 ARG cc_start: 0.7670 (pmm-80) cc_final: 0.7396 (mpp80) REVERT: A 203 ILE cc_start: 0.8398 (mt) cc_final: 0.8147 (mp) REVERT: A 211 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.7297 (mtm-85) REVERT: A 213 TYR cc_start: 0.8692 (m-80) cc_final: 0.8296 (m-80) REVERT: B 42 ARG cc_start: 0.7427 (ttp80) cc_final: 0.7128 (ttp80) REVERT: B 186 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: B 237 ASN cc_start: 0.8507 (t0) cc_final: 0.8273 (t160) REVERT: B 239 ASN cc_start: 0.8250 (m110) cc_final: 0.7882 (m110) REVERT: B 258 ASP cc_start: 0.8072 (t0) cc_final: 0.7380 (t0) REVERT: B 314 ARG cc_start: 0.8104 (ptm160) cc_final: 0.7863 (ptm160) REVERT: B 340 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7784 (t0) REVERT: R 58 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7951 (tp) REVERT: R 72 PHE cc_start: 0.7332 (t80) cc_final: 0.6976 (t80) REVERT: R 120 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7857 (mm) outliers start: 26 outliers final: 15 residues processed: 240 average time/residue: 0.5974 time to fit residues: 152.2558 Evaluate side-chains 247 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 75 GLN B 119 ASN B 142 HIS B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.134285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118491 restraints weight = 12048.624| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.05 r_work: 0.3385 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8547 Z= 0.214 Angle : 0.634 8.226 11576 Z= 0.331 Chirality : 0.044 0.190 1307 Planarity : 0.004 0.047 1450 Dihedral : 4.534 35.047 1211 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.85 % Favored : 95.95 % Rotamer: Outliers : 2.98 % Allowed : 28.48 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1038 helix: 2.51 (0.23), residues: 440 sheet: -0.01 (0.36), residues: 207 loop : -1.01 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 191 TYR 0.015 0.002 TYR N 96 PHE 0.040 0.002 PHE N 69 TRP 0.019 0.002 TRP B 99 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 8545) covalent geometry : angle 0.63186 (11572) SS BOND : bond 0.00399 ( 2) SS BOND : angle 2.97338 ( 4) hydrogen bonds : bond 0.04421 ( 480) hydrogen bonds : angle 4.45040 ( 1374) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7690 (pmm-80) cc_final: 0.7400 (mpp80) REVERT: A 203 ILE cc_start: 0.8465 (mt) cc_final: 0.8221 (mp) REVERT: A 211 ARG cc_start: 0.7701 (mtm-85) cc_final: 0.7309 (mtm-85) REVERT: B 42 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7197 (ttp80) REVERT: B 72 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8180 (p) REVERT: B 119 ASN cc_start: 0.8246 (m-40) cc_final: 0.7966 (m110) REVERT: B 186 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: B 258 ASP cc_start: 0.8072 (t0) cc_final: 0.7352 (t0) REVERT: R 58 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7949 (tp) REVERT: R 72 PHE cc_start: 0.7355 (t80) cc_final: 0.7013 (t80) REVERT: R 120 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7885 (mm) outliers start: 27 outliers final: 15 residues processed: 237 average time/residue: 0.6159 time to fit residues: 154.6096 Evaluate side-chains 240 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 221 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 15 optimal weight: 0.1980 chunk 36 optimal weight: 0.0070 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 73 optimal weight: 0.2980 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 75 GLN B 155 ASN B 237 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.136610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.120662 restraints weight = 12174.155| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.06 r_work: 0.3429 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8547 Z= 0.139 Angle : 0.588 7.651 11576 Z= 0.306 Chirality : 0.042 0.188 1307 Planarity : 0.004 0.040 1450 Dihedral : 4.388 34.996 1211 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.15 % Rotamer: Outliers : 2.54 % Allowed : 29.14 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.26), residues: 1038 helix: 2.71 (0.24), residues: 439 sheet: 0.02 (0.37), residues: 202 loop : -1.02 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 38 TYR 0.014 0.001 TYR B 124 PHE 0.033 0.002 PHE N 69 TRP 0.020 0.002 TRP B 99 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8545) covalent geometry : angle 0.58674 (11572) SS BOND : bond 0.00359 ( 2) SS BOND : angle 2.40371 ( 4) hydrogen bonds : bond 0.03979 ( 480) hydrogen bonds : angle 4.35833 ( 1374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3558.20 seconds wall clock time: 61 minutes 33.70 seconds (3693.70 seconds total)