Starting phenix.real_space_refine on Wed Jan 15 11:31:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xql_38580/01_2025/8xql_38580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xql_38580/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xql_38580/01_2025/8xql_38580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xql_38580/01_2025/8xql_38580.map" model { file = "/net/cci-nas-00/data/ceres_data/8xql_38580/01_2025/8xql_38580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xql_38580/01_2025/8xql_38580.cif" } resolution = 2.99 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.38, per 1000 atoms: 0.64 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: 2.29 Conformation dependent library (CDL) restraints added in 833.1 milliseconds 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: 1.05 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: 2.60 Time building geometry restraints manager: 2.47 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: 0.900 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.820 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.060 ------------------------------------------------------------------------------- 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 8545 Z= 0.329 Angle : 0.628 10.001 11572 Z= 0.330 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 : 14.24 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 (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: 0.98 (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 TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS R 151 PHE 0.023 0.002 PHE A 87 TYR 0.016 0.002 TYR N 96 ARG 0.005 0.000 ARG B 314 *********************** 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 : 0.700 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: 1.2149 time to fit residues: 288.8250 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 : 0.902 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.135465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119837 restraints weight = 11995.942| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.04 r_work: 0.3406 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8545 Z= 0.266 Angle : 0.570 7.921 11572 Z= 0.301 Chirality : 0.042 0.179 1307 Planarity : 0.004 0.049 1450 Dihedral : 4.474 34.211 1213 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.14 % Favored : 95.66 % Rotamer: Outliers : 4.64 % Allowed : 22.30 % Favored : 73.07 % 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: 1.16 (0.26), residues: 1038 helix: 2.53 (0.23), residues: 440 sheet: -0.05 (0.36), residues: 210 loop : -0.83 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.004 0.001 HIS A 212 PHE 0.019 0.002 PHE A 87 TYR 0.014 0.001 TYR N 96 ARG 0.005 0.000 ARG A 97 *********************** 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 271 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7461 (mtm-85) REVERT: A 134 ASN cc_start: 0.7505 (m-40) cc_final: 0.7154 (m-40) REVERT: B 100 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8137 (p) REVERT: B 119 ASN cc_start: 0.8322 (m-40) cc_final: 0.8085 (m110) REVERT: B 186 ASP cc_start: 0.7666 (m-30) cc_final: 0.7384 (m-30) REVERT: B 212 ASP cc_start: 0.7972 (t0) cc_final: 0.7705 (t0) REVERT: B 258 ASP cc_start: 0.8109 (t0) cc_final: 0.7627 (t0) REVERT: B 314 ARG cc_start: 0.8222 (ptm160) cc_final: 0.7949 (ptm160) REVERT: R 17 PHE cc_start: 0.8338 (t80) cc_final: 0.7935 (t80) REVERT: R 72 PHE cc_start: 0.7557 (t80) cc_final: 0.7355 (t80) REVERT: R 120 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7897 (mm) outliers start: 42 outliers final: 15 residues processed: 242 average time/residue: 1.2274 time to fit residues: 315.6384 Evaluate side-chains 241 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 223 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 70 optimal weight: 0.4980 chunk 41 optimal weight: 0.0060 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.135501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.119652 restraints weight = 12081.306| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.06 r_work: 0.3417 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8545 Z= 0.208 Angle : 0.537 7.462 11572 Z= 0.284 Chirality : 0.041 0.188 1307 Planarity : 0.004 0.037 1450 Dihedral : 4.344 34.894 1211 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 3.75 % Allowed : 23.51 % Favored : 72.74 % 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: 1.25 (0.26), residues: 1038 helix: 2.67 (0.23), residues: 439 sheet: -0.01 (0.35), residues: 217 loop : -0.88 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.003 0.001 HIS A 212 PHE 0.019 0.002 PHE R 82 TYR 0.011 0.001 TYR N 96 ARG 0.005 0.000 ARG B 251 *********************** 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 258 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7427 (mtm-85) REVERT: A 236 ASP cc_start: 0.8801 (t70) cc_final: 0.8531 (t0) REVERT: B 46 ARG cc_start: 0.8468 (mtt-85) cc_final: 0.8216 (mtp-110) REVERT: B 176 GLN cc_start: 0.8596 (mt0) cc_final: 0.8388 (mt0) REVERT: B 186 ASP cc_start: 0.7634 (m-30) cc_final: 0.7326 (m-30) REVERT: B 258 ASP cc_start: 0.8086 (t0) cc_final: 0.7507 (t0) REVERT: B 283 ARG cc_start: 0.8450 (tpt-90) cc_final: 0.8224 (tpt90) REVERT: B 314 ARG cc_start: 0.8092 (ptm160) cc_final: 0.7822 (ptm160) REVERT: R 17 PHE cc_start: 0.8460 (t80) cc_final: 0.7950 (t80) REVERT: R 72 PHE cc_start: 0.7520 (t80) cc_final: 0.7233 (t80) REVERT: R 120 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7866 (mm) outliers start: 34 outliers final: 15 residues processed: 236 average time/residue: 1.2136 time to fit residues: 304.1774 Evaluate side-chains 240 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 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 59 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 237 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.132337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116439 restraints weight = 12224.508| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.05 r_work: 0.3373 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8545 Z= 0.317 Angle : 0.582 8.350 11572 Z= 0.304 Chirality : 0.042 0.175 1307 Planarity : 0.004 0.040 1450 Dihedral : 4.485 34.853 1211 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.47 % Rotamer: Outliers : 4.30 % Allowed : 23.84 % Favored : 71.85 % 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: 1.15 (0.26), residues: 1038 helix: 2.50 (0.23), residues: 441 sheet: 0.11 (0.36), residues: 207 loop : -0.93 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS A 212 PHE 0.021 0.002 PHE R 82 TYR 0.016 0.001 TYR N 96 ARG 0.005 0.000 ARG B 219 *********************** 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 263 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7464 (mtm-85) REVERT: B 46 ARG cc_start: 0.8409 (mtt-85) cc_final: 0.8158 (mtp-110) REVERT: B 186 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: B 258 ASP cc_start: 0.8158 (t0) cc_final: 0.7537 (t0) REVERT: N 87 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.8016 (mt) REVERT: R 17 PHE cc_start: 0.8578 (t80) cc_final: 0.7934 (t80) REVERT: R 72 PHE cc_start: 0.7545 (t80) cc_final: 0.7198 (t80) REVERT: R 120 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7934 (mm) outliers start: 39 outliers final: 17 residues processed: 242 average time/residue: 1.2213 time to fit residues: 313.8149 Evaluate side-chains 235 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 163 ILE 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 44 GLN 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 N residue 72 SER Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain R residue 120 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 75 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 119 ASN B 142 HIS B 155 ASN B 176 GLN B 237 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.132793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116800 restraints weight = 12097.823| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.04 r_work: 0.3387 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8545 Z= 0.253 Angle : 0.567 8.490 11572 Z= 0.296 Chirality : 0.042 0.192 1307 Planarity : 0.004 0.051 1450 Dihedral : 4.460 34.990 1211 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.05 % Rotamer: Outliers : 3.97 % Allowed : 24.61 % Favored : 71.41 % 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: 1.18 (0.26), residues: 1038 helix: 2.57 (0.23), residues: 440 sheet: 0.14 (0.36), residues: 208 loop : -0.98 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.003 0.001 HIS A 212 PHE 0.023 0.002 PHE A 87 TYR 0.013 0.001 TYR N 96 ARG 0.005 0.000 ARG A 138 *********************** 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: 36 poor density : 223 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7490 (mtm-85) REVERT: A 201 LEU cc_start: 0.8109 (mm) cc_final: 0.7898 (mm) REVERT: A 203 ILE cc_start: 0.8381 (mt) cc_final: 0.8132 (mp) REVERT: B 46 ARG cc_start: 0.8401 (mtt-85) cc_final: 0.8162 (mtp-110) REVERT: B 186 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: B 258 ASP cc_start: 0.8118 (t0) cc_final: 0.7479 (t0) REVERT: R 17 PHE cc_start: 0.8478 (t80) cc_final: 0.8162 (t80) REVERT: R 58 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7886 (tp) REVERT: R 72 PHE cc_start: 0.7484 (t80) cc_final: 0.7119 (t80) outliers start: 36 outliers final: 16 residues processed: 239 average time/residue: 1.1848 time to fit residues: 300.8135 Evaluate side-chains 234 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 198 LEU 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 C residue 21 MET Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 58 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 82 optimal weight: 0.0770 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.0370 chunk 73 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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 88 ASN B 119 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 = 0.3770 r_free = 0.3770 target = 0.134734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.119095 restraints weight = 12072.391| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.06 r_work: 0.3421 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8545 Z= 0.186 Angle : 0.547 7.934 11572 Z= 0.286 Chirality : 0.041 0.185 1307 Planarity : 0.004 0.051 1450 Dihedral : 4.315 34.862 1211 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Rotamer: Outliers : 2.87 % Allowed : 26.93 % 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 (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: 1.22 (0.26), residues: 1038 helix: 2.66 (0.23), residues: 439 sheet: 0.02 (0.35), residues: 216 loop : -0.96 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.003 0.001 HIS A 212 PHE 0.024 0.002 PHE R 82 TYR 0.010 0.001 TYR N 96 ARG 0.005 0.000 ARG A 138 *********************** 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 256 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7459 (mtm-85) REVERT: A 182 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 202 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7683 (ttp-110) REVERT: A 203 ILE cc_start: 0.8356 (mt) cc_final: 0.8114 (mp) REVERT: A 211 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7298 (mtm-85) REVERT: B 42 ARG cc_start: 0.7477 (ttp80) cc_final: 0.7197 (ttp80) REVERT: B 119 ASN cc_start: 0.7970 (m-40) cc_final: 0.7697 (m110) REVERT: B 186 ASP cc_start: 0.7594 (m-30) cc_final: 0.7287 (m-30) REVERT: B 237 ASN cc_start: 0.8474 (t0) cc_final: 0.8230 (t160) REVERT: B 239 ASN cc_start: 0.8149 (m110) cc_final: 0.7757 (m110) REVERT: B 258 ASP cc_start: 0.8047 (t0) cc_final: 0.7368 (t0) REVERT: B 314 ARG cc_start: 0.8090 (ptm160) cc_final: 0.7855 (ptm160) REVERT: R 17 PHE cc_start: 0.8276 (t80) cc_final: 0.7878 (t80) REVERT: R 72 PHE cc_start: 0.7428 (t80) cc_final: 0.7078 (t80) outliers start: 26 outliers final: 12 residues processed: 240 average time/residue: 1.2167 time to fit residues: 310.6941 Evaluate side-chains 232 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 327 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 5 ILE 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 81 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 0.0670 chunk 57 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 92 optimal weight: 0.0870 chunk 75 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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 88 ASN B 259 GLN B 295 ASN B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.134866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119334 restraints weight = 12057.410| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.05 r_work: 0.3408 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8545 Z= 0.228 Angle : 0.572 8.466 11572 Z= 0.296 Chirality : 0.042 0.184 1307 Planarity : 0.004 0.039 1450 Dihedral : 4.350 34.792 1211 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 4.08 % Allowed : 25.83 % Favored : 70.09 % 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: 1.22 (0.26), residues: 1038 helix: 2.69 (0.23), residues: 437 sheet: 0.09 (0.36), residues: 202 loop : -0.98 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 212 PHE 0.024 0.002 PHE R 82 TYR 0.012 0.001 TYR N 96 ARG 0.006 0.000 ARG A 138 *********************** 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 261 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7398 (mtm-85) REVERT: A 182 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7393 (mm-30) REVERT: A 201 LEU cc_start: 0.8030 (mm) cc_final: 0.7797 (mm) REVERT: A 203 ILE cc_start: 0.8403 (mt) cc_final: 0.8135 (mp) REVERT: A 211 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.7285 (mtm-85) REVERT: A 236 ASP cc_start: 0.8757 (t70) cc_final: 0.8419 (t0) REVERT: B 37 ILE cc_start: 0.7941 (mm) cc_final: 0.7631 (mt) REVERT: B 72 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8158 (p) REVERT: B 119 ASN cc_start: 0.8259 (m-40) cc_final: 0.8044 (m110) REVERT: B 186 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7378 (m-30) REVERT: B 237 ASN cc_start: 0.8483 (t0) cc_final: 0.8169 (t160) REVERT: B 239 ASN cc_start: 0.8164 (m110) cc_final: 0.7764 (m110) REVERT: B 258 ASP cc_start: 0.8065 (t0) cc_final: 0.7383 (t0) REVERT: B 314 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7896 (ptm160) REVERT: R 58 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7959 (tp) REVERT: R 72 PHE cc_start: 0.7431 (t80) cc_final: 0.7068 (t80) outliers start: 37 outliers final: 17 residues processed: 241 average time/residue: 1.1521 time to fit residues: 295.4470 Evaluate side-chains 239 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 218 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 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 198 LEU 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 N residue 49 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 58 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 78 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 142 HIS B 155 ASN B 259 GLN B 340 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.134318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118587 restraints weight = 12142.217| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.05 r_work: 0.3400 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8545 Z= 0.259 Angle : 0.598 8.568 11572 Z= 0.312 Chirality : 0.043 0.184 1307 Planarity : 0.004 0.039 1450 Dihedral : 4.420 34.725 1211 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 3.31 % Allowed : 27.26 % Favored : 69.43 % 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: 1.13 (0.26), residues: 1038 helix: 2.57 (0.23), residues: 439 sheet: 0.05 (0.36), residues: 202 loop : -1.01 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS A 212 PHE 0.039 0.002 PHE R 17 TYR 0.014 0.001 TYR N 96 ARG 0.007 0.000 ARG B 251 *********************** 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 263 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7436 (mtm-85) REVERT: A 182 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7377 (mm-30) REVERT: A 201 LEU cc_start: 0.8062 (mm) cc_final: 0.7818 (mm) REVERT: A 203 ILE cc_start: 0.8435 (mt) cc_final: 0.8172 (mp) REVERT: A 211 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7267 (mtm-85) REVERT: B 37 ILE cc_start: 0.7946 (mm) cc_final: 0.7683 (mt) REVERT: B 72 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 119 ASN cc_start: 0.8367 (m-40) cc_final: 0.8140 (m110) REVERT: B 186 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7469 (m-30) REVERT: B 258 ASP cc_start: 0.8054 (t0) cc_final: 0.7385 (t0) REVERT: B 340 ASN cc_start: 0.7836 (t0) cc_final: 0.7581 (t0) REVERT: R 58 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7949 (tp) REVERT: R 72 PHE cc_start: 0.7404 (t80) cc_final: 0.7058 (t80) outliers start: 30 outliers final: 17 residues processed: 245 average time/residue: 1.1715 time to fit residues: 305.5291 Evaluate side-chains 252 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 182 GLU 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 198 LEU 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 B residue 338 ILE Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 58 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 142 HIS B 237 ASN B 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.134146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118291 restraints weight = 12179.679| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.07 r_work: 0.3405 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8545 Z= 0.250 Angle : 0.600 7.984 11572 Z= 0.312 Chirality : 0.043 0.183 1307 Planarity : 0.004 0.038 1450 Dihedral : 4.430 34.875 1211 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 2.87 % Allowed : 28.48 % Favored : 68.65 % 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: 1038 helix: 2.58 (0.23), residues: 439 sheet: -0.02 (0.36), residues: 202 loop : -1.03 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS A 212 PHE 0.038 0.002 PHE R 17 TYR 0.013 0.001 TYR N 96 ARG 0.009 0.001 ARG B 219 *********************** 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 253 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7465 (mtm-85) REVERT: A 201 LEU cc_start: 0.8074 (mm) cc_final: 0.7826 (mm) REVERT: A 203 ILE cc_start: 0.8419 (mt) cc_final: 0.8153 (mp) REVERT: A 211 ARG cc_start: 0.7702 (mtm-85) cc_final: 0.7283 (mtm-85) REVERT: B 37 ILE cc_start: 0.7997 (mm) cc_final: 0.7778 (OUTLIER) REVERT: B 42 ARG cc_start: 0.7487 (ttp80) cc_final: 0.7189 (ttp80) REVERT: B 72 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8172 (p) REVERT: B 119 ASN cc_start: 0.8331 (m-40) cc_final: 0.8112 (m110) REVERT: B 186 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: B 237 ASN cc_start: 0.8567 (t0) cc_final: 0.8322 (t160) REVERT: B 239 ASN cc_start: 0.8203 (m110) cc_final: 0.7844 (m110) REVERT: B 258 ASP cc_start: 0.8058 (t0) cc_final: 0.7261 (t0) REVERT: B 340 ASN cc_start: 0.7833 (t0) cc_final: 0.7566 (t0) REVERT: R 58 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7931 (tp) REVERT: R 72 PHE cc_start: 0.7388 (t80) cc_final: 0.7054 (t80) outliers start: 26 outliers final: 19 residues processed: 239 average time/residue: 1.1690 time to fit residues: 297.5416 Evaluate side-chains 249 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR 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 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 198 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 58 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 27 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 142 HIS B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117452 restraints weight = 12059.205| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.04 r_work: 0.3375 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8545 Z= 0.344 Angle : 0.644 8.217 11572 Z= 0.336 Chirality : 0.045 0.192 1307 Planarity : 0.004 0.041 1450 Dihedral : 4.659 35.102 1211 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 3.09 % Allowed : 28.59 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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 (0.26), residues: 1038 helix: 2.39 (0.23), residues: 441 sheet: -0.13 (0.36), residues: 202 loop : -1.09 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS A 212 PHE 0.044 0.002 PHE N 69 TYR 0.016 0.002 TYR N 96 ARG 0.009 0.001 ARG A 97 ********************** 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 257 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7731 (pmm-80) cc_final: 0.7438 (mpp80) REVERT: A 201 LEU cc_start: 0.8096 (mm) cc_final: 0.7829 (mm) REVERT: A 203 ILE cc_start: 0.8468 (mt) cc_final: 0.8221 (mp) REVERT: B 72 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8201 (p) REVERT: B 186 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: B 258 ASP cc_start: 0.8079 (t0) cc_final: 0.7399 (t0) REVERT: B 340 ASN cc_start: 0.7838 (t0) cc_final: 0.7553 (t0) REVERT: R 58 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7976 (tp) REVERT: R 72 PHE cc_start: 0.7395 (t80) cc_final: 0.7043 (t80) outliers start: 28 outliers final: 21 residues processed: 243 average time/residue: 1.1971 time to fit residues: 309.0217 Evaluate side-chains 247 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR 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 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 198 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 58 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 Chi-restraints excluded: chain R residue 270 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 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 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 75 GLN B 119 ASN B 142 HIS B 155 ASN B 237 ASN B 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.133363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.117673 restraints weight = 12230.438| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.05 r_work: 0.3384 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8545 Z= 0.311 Angle : 0.636 7.919 11572 Z= 0.333 Chirality : 0.044 0.192 1307 Planarity : 0.004 0.050 1450 Dihedral : 4.682 35.010 1211 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.05 % Rotamer: Outliers : 3.31 % Allowed : 28.48 % Favored : 68.21 % 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: 0.89 (0.26), residues: 1038 helix: 2.40 (0.23), residues: 440 sheet: -0.16 (0.36), residues: 202 loop : -1.12 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS A 212 PHE 0.042 0.002 PHE N 69 TYR 0.014 0.002 TYR N 96 ARG 0.011 0.001 ARG A 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6958.55 seconds wall clock time: 123 minutes 31.96 seconds (7411.96 seconds total)