Starting phenix.real_space_refine on Sat Aug 3 21:02:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqo_38583/08_2024/8xqo_38583.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqo_38583/08_2024/8xqo_38583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqo_38583/08_2024/8xqo_38583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqo_38583/08_2024/8xqo_38583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqo_38583/08_2024/8xqo_38583.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqo_38583/08_2024/8xqo_38583.cif" } resolution = 2.77 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= 0.023 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 59 5.16 5 C 5736 2.51 5 N 1512 2.21 5 O 1651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8958 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 3, 'TRANS': 277} Chain breaks: 2 Chain: "R" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'CLR': 1, 'GOQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.67, per 1000 atoms: 0.63 Number of scatterers: 8958 At special positions: 0 Unit cell: (89.44, 119.6, 125.84, 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 59 16.00 O 1651 8.00 N 1512 7.00 C 5736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.81 Conformation dependent library (CDL) restraints added in 1.6 seconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 39.6% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.632A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.604A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.556A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.164A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 208 through 212 Processing helix chain 'R' and resid 3 through 37 Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 80 through 112 Processing helix chain 'R' and resid 116 through 124 Processing helix chain 'R' and resid 125 through 137 Processing helix chain 'R' and resid 137 through 162 Processing helix chain 'R' and resid 173 through 216 Proline residue: R 190 - end of helix Processing helix chain 'R' and resid 227 through 253 Processing helix chain 'R' and resid 260 through 284 removed outlier: 4.236A pdb=" N TYR R 272 " --> pdb=" O MET R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 4.229A 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 185 through 190 removed outlier: 3.567A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.885A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.752A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.317A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.247A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.869A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.329A 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: 6.452A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.584A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.654A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.654A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.514A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.757A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1383 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: 2.74 Time building geometry restraints manager: 4.13 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: 2845 1.34 - 1.46: 1634 1.46 - 1.57: 4582 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 9148 Sorted by residual: bond pdb=" C8 GOQ R 501 " pdb=" C9 GOQ R 501 " ideal model delta sigma weight residual 1.350 1.386 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C5 GOQ R 501 " pdb=" C6 GOQ R 501 " ideal model delta sigma weight residual 1.454 1.421 0.033 2.00e-02 2.50e+03 2.67e+00 bond pdb=" C10 GOQ R 501 " pdb=" C9 GOQ R 501 " ideal model delta sigma weight residual 1.423 1.393 0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" O GOQ R 501 " pdb=" C1 GOQ R 501 " ideal model delta sigma weight residual 1.340 1.367 -0.027 2.00e-02 2.50e+03 1.89e+00 bond pdb=" CB MET R 212 " pdb=" CG MET R 212 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.75e+00 ... (remaining 9143 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.64: 110 105.64 - 112.73: 4957 112.73 - 119.82: 2836 119.82 - 126.90: 4365 126.90 - 133.99: 112 Bond angle restraints: 12380 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 112.96 108.57 4.39 1.00e+00 1.00e+00 1.93e+01 angle pdb=" CB MET R 212 " pdb=" CG MET R 212 " pdb=" SD MET R 212 " ideal model delta sigma weight residual 112.70 100.88 11.82 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CA LEU R 75 " pdb=" CB LEU R 75 " pdb=" CG LEU R 75 " ideal model delta sigma weight residual 116.30 129.98 -13.68 3.50e+00 8.16e-02 1.53e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 127.55 -6.01 1.91e+00 2.74e-01 9.90e+00 angle pdb=" C PHE R 72 " pdb=" CA PHE R 72 " pdb=" CB PHE R 72 " ideal model delta sigma weight residual 111.15 116.02 -4.87 1.65e+00 3.67e-01 8.70e+00 ... (remaining 12375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4732 17.58 - 35.15: 553 35.15 - 52.73: 140 52.73 - 70.31: 16 70.31 - 87.88: 5 Dihedral angle restraints: 5446 sinusoidal: 2171 harmonic: 3275 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 63.53 29.47 1 1.00e+01 1.00e-02 1.24e+01 dihedral pdb=" CB GLU A 207 " pdb=" CG GLU A 207 " pdb=" CD GLU A 207 " pdb=" OE1 GLU A 207 " ideal model delta sinusoidal sigma weight residual 0.00 -87.88 87.88 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA GLU S 222 " pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta harmonic sigma weight residual -180.00 -164.18 -15.82 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 5443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1103 0.045 - 0.090: 224 0.090 - 0.135: 72 0.135 - 0.180: 7 0.180 - 0.225: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CB ILE R 152 " pdb=" CA ILE R 152 " pdb=" CG1 ILE R 152 " pdb=" CG2 ILE R 152 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 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 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA MET R 212 " pdb=" N MET R 212 " pdb=" C MET R 212 " pdb=" CB MET R 212 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 1405 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 72 " 0.052 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO R 73 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO R 73 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 73 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO S 107 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO S 224 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " 0.030 5.00e-02 4.00e+02 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 39 2.46 - 3.07: 6038 3.07 - 3.68: 13968 3.68 - 4.29: 20716 4.29 - 4.90: 34679 Nonbonded interactions: 75440 Sorted by model distance: nonbonded pdb=" O LEU R 75 " pdb=" OG1 THR R 78 " model vdw 1.853 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.074 3.040 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.137 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.197 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.242 3.040 ... (remaining 75435 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 : 0.003 0.059 9148 Z= 0.209 Angle : 0.567 13.684 12380 Z= 0.285 Chirality : 0.041 0.225 1408 Planarity : 0.004 0.080 1540 Dihedral : 15.538 87.884 3322 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.10 % Allowed : 29.04 % 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 (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: 1.14 (0.26), residues: 1114 helix: 2.52 (0.24), residues: 429 sheet: -0.24 (0.32), residues: 267 loop : -0.39 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 98 HIS 0.003 0.001 HIS R 151 PHE 0.013 0.001 PHE R 106 TYR 0.025 0.001 TYR S 223 ARG 0.007 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 0.979 Fit side-chains REVERT: A 310 LEU cc_start: 0.8782 (mp) cc_final: 0.8556 (mt) REVERT: S 82 GLN cc_start: 0.8342 (tp40) cc_final: 0.8078 (tp-100) outliers start: 1 outliers final: 4 residues processed: 251 average time/residue: 1.1251 time to fit residues: 301.6958 Evaluate side-chains 242 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 238 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 146 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9148 Z= 0.420 Angle : 0.611 13.804 12380 Z= 0.320 Chirality : 0.045 0.221 1408 Planarity : 0.005 0.079 1540 Dihedral : 5.422 59.104 1294 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.83 % Allowed : 23.31 % 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 (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: 0.88 (0.25), residues: 1114 helix: 2.26 (0.24), residues: 428 sheet: -0.36 (0.30), residues: 270 loop : -0.47 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.005 0.001 HIS B 91 PHE 0.018 0.002 PHE R 248 TYR 0.028 0.002 TYR S 223 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 241 time to evaluate : 1.074 Fit side-chains REVERT: A 28 GLU cc_start: 0.7179 (tp30) cc_final: 0.6914 (tp30) REVERT: B 19 ARG cc_start: 0.7481 (ttm-80) cc_final: 0.7195 (ttm-80) REVERT: B 159 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8470 (p) REVERT: B 197 ARG cc_start: 0.7803 (tpp80) cc_final: 0.7315 (mmm-85) REVERT: B 227 SER cc_start: 0.8717 (m) cc_final: 0.8204 (t) REVERT: B 233 CYS cc_start: 0.8338 (t) cc_final: 0.8095 (p) REVERT: S 142 SER cc_start: 0.8244 (m) cc_final: 0.8030 (p) outliers start: 57 outliers final: 26 residues processed: 266 average time/residue: 1.0776 time to fit residues: 307.8549 Evaluate side-chains 255 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 228 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 77 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9148 Z= 0.240 Angle : 0.552 14.114 12380 Z= 0.286 Chirality : 0.042 0.201 1408 Planarity : 0.004 0.071 1540 Dihedral : 5.166 55.437 1288 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.21 % Allowed : 24.74 % Favored : 70.04 % 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: 0.90 (0.25), residues: 1114 helix: 2.36 (0.24), residues: 429 sheet: -0.45 (0.30), residues: 276 loop : -0.51 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 213 PHE 0.018 0.001 PHE R 82 TYR 0.026 0.001 TYR S 223 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 239 time to evaluate : 1.084 Fit side-chains REVERT: A 28 GLU cc_start: 0.7143 (tp30) cc_final: 0.6869 (tp30) REVERT: A 184 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8396 (tt) REVERT: A 192 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8107 (mptm) REVERT: A 271 LYS cc_start: 0.7994 (ptmm) cc_final: 0.7770 (ttpt) REVERT: A 289 GLU cc_start: 0.7301 (tm-30) cc_final: 0.7058 (tm-30) REVERT: A 324 THR cc_start: 0.7793 (p) cc_final: 0.7570 (t) REVERT: B 19 ARG cc_start: 0.7475 (ttm-80) cc_final: 0.7185 (ttm-80) REVERT: B 37 ILE cc_start: 0.8766 (tt) cc_final: 0.8313 (pt) REVERT: B 197 ARG cc_start: 0.7737 (tpp80) cc_final: 0.7292 (mmm-85) REVERT: B 227 SER cc_start: 0.8723 (m) cc_final: 0.8178 (t) REVERT: B 233 CYS cc_start: 0.8356 (t) cc_final: 0.8150 (p) REVERT: S 142 SER cc_start: 0.8222 (m) cc_final: 0.7991 (p) REVERT: R 105 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8337 (m) outliers start: 51 outliers final: 23 residues processed: 261 average time/residue: 1.0601 time to fit residues: 296.6998 Evaluate side-chains 260 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 147 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.0070 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 220 GLN S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9148 Z= 0.211 Angle : 0.548 18.271 12380 Z= 0.277 Chirality : 0.041 0.182 1408 Planarity : 0.004 0.062 1540 Dihedral : 5.116 58.018 1288 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 6.13 % Allowed : 24.74 % Favored : 69.12 % 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 (0.25), residues: 1114 helix: 2.40 (0.24), residues: 429 sheet: -0.52 (0.29), residues: 283 loop : -0.50 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS A 213 PHE 0.014 0.001 PHE R 188 TYR 0.022 0.001 TYR S 223 ARG 0.007 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 246 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7241 (tp30) cc_final: 0.6973 (tp30) REVERT: A 184 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8327 (tt) REVERT: A 192 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8000 (mptm) REVERT: A 231 ASP cc_start: 0.7718 (t0) cc_final: 0.7403 (t0) REVERT: A 271 LYS cc_start: 0.7994 (ptmm) cc_final: 0.7793 (ttpt) REVERT: A 275 GLU cc_start: 0.7363 (tp30) cc_final: 0.6989 (tp30) REVERT: A 289 GLU cc_start: 0.7328 (tm-30) cc_final: 0.7042 (tm-30) REVERT: B 19 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.7182 (ttm-80) REVERT: B 32 GLN cc_start: 0.8446 (mt0) cc_final: 0.8104 (mt0) REVERT: B 35 ASN cc_start: 0.8046 (t0) cc_final: 0.7745 (t0) REVERT: B 37 ILE cc_start: 0.8749 (tt) cc_final: 0.8306 (pt) REVERT: B 177 THR cc_start: 0.8481 (m) cc_final: 0.8151 (p) REVERT: B 197 ARG cc_start: 0.7695 (tpp80) cc_final: 0.7218 (mmm-85) REVERT: B 217 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7705 (ppp) REVERT: S 142 SER cc_start: 0.8245 (m) cc_final: 0.7962 (p) REVERT: S 179 ARG cc_start: 0.8246 (mpt-90) cc_final: 0.7777 (mpp80) REVERT: S 234 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: R 76 PHE cc_start: 0.6472 (OUTLIER) cc_final: 0.6168 (m-10) REVERT: R 105 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8318 (m) outliers start: 60 outliers final: 26 residues processed: 275 average time/residue: 1.0560 time to fit residues: 311.9751 Evaluate side-chains 262 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 230 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 179 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 0.0670 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 220 GLN B 293 ASN B 340 ASN S 77 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9148 Z= 0.300 Angle : 0.564 16.586 12380 Z= 0.289 Chirality : 0.043 0.197 1408 Planarity : 0.004 0.060 1540 Dihedral : 5.247 58.613 1288 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 6.13 % Allowed : 24.85 % Favored : 69.02 % 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: 0.82 (0.25), residues: 1114 helix: 2.25 (0.24), residues: 431 sheet: -0.54 (0.30), residues: 278 loop : -0.45 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS A 213 PHE 0.014 0.002 PHE R 76 TYR 0.025 0.001 TYR S 223 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 224 time to evaluate : 1.044 Fit side-chains REVERT: A 28 GLU cc_start: 0.7164 (tp30) cc_final: 0.6887 (tp30) REVERT: A 184 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8315 (tt) REVERT: A 231 ASP cc_start: 0.7743 (t0) cc_final: 0.7417 (t0) REVERT: A 271 LYS cc_start: 0.7938 (ptmm) cc_final: 0.7734 (ttpt) REVERT: A 275 GLU cc_start: 0.7406 (tp30) cc_final: 0.7062 (tp30) REVERT: A 289 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7061 (tm-30) REVERT: B 19 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.7179 (ttm-80) REVERT: B 32 GLN cc_start: 0.8422 (mt0) cc_final: 0.8114 (mt0) REVERT: B 35 ASN cc_start: 0.8010 (t0) cc_final: 0.7705 (t0) REVERT: B 37 ILE cc_start: 0.8771 (tt) cc_final: 0.8390 (pt) REVERT: B 177 THR cc_start: 0.8488 (m) cc_final: 0.8162 (p) REVERT: B 197 ARG cc_start: 0.7713 (tpp80) cc_final: 0.7283 (mmm-85) REVERT: B 227 SER cc_start: 0.8723 (m) cc_final: 0.8175 (t) REVERT: B 234 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8496 (t80) REVERT: S 142 SER cc_start: 0.8302 (m) cc_final: 0.8037 (p) REVERT: S 179 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7802 (mpp80) REVERT: S 234 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6477 (mp0) REVERT: R 76 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.5896 (m-80) outliers start: 60 outliers final: 30 residues processed: 256 average time/residue: 1.0724 time to fit residues: 294.3423 Evaluate side-chains 258 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 223 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 220 GLN B 340 ASN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9148 Z= 0.242 Angle : 0.554 16.031 12380 Z= 0.281 Chirality : 0.041 0.190 1408 Planarity : 0.004 0.060 1540 Dihedral : 5.211 59.929 1288 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.52 % Allowed : 26.58 % Favored : 67.89 % 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: 0.84 (0.25), residues: 1114 helix: 2.29 (0.24), residues: 431 sheet: -0.57 (0.30), residues: 278 loop : -0.43 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 213 PHE 0.014 0.001 PHE R 76 TYR 0.025 0.001 TYR S 223 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 230 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7157 (tp30) cc_final: 0.6875 (tp30) REVERT: A 184 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8325 (tt) REVERT: A 192 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7992 (mptm) REVERT: A 231 ASP cc_start: 0.7714 (t0) cc_final: 0.7370 (t0) REVERT: A 275 GLU cc_start: 0.7350 (tp30) cc_final: 0.7034 (tp30) REVERT: A 289 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7053 (tm-30) REVERT: B 19 ARG cc_start: 0.7465 (ttm-80) cc_final: 0.7159 (ttm-80) REVERT: B 22 ARG cc_start: 0.8539 (mtt180) cc_final: 0.8270 (mtt180) REVERT: B 32 GLN cc_start: 0.8419 (mt0) cc_final: 0.8110 (mt0) REVERT: B 35 ASN cc_start: 0.8000 (t0) cc_final: 0.7691 (t0) REVERT: B 37 ILE cc_start: 0.8764 (tt) cc_final: 0.8386 (pt) REVERT: B 68 ARG cc_start: 0.8762 (ttt-90) cc_final: 0.8379 (tpp80) REVERT: B 177 THR cc_start: 0.8477 (m) cc_final: 0.8139 (p) REVERT: S 142 SER cc_start: 0.8269 (m) cc_final: 0.8019 (p) REVERT: S 179 ARG cc_start: 0.8263 (mpt-90) cc_final: 0.7779 (mpp80) REVERT: S 234 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6461 (mp0) REVERT: R 76 PHE cc_start: 0.6374 (OUTLIER) cc_final: 0.5874 (m-80) outliers start: 54 outliers final: 33 residues processed: 259 average time/residue: 1.1924 time to fit residues: 328.7346 Evaluate side-chains 266 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 229 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 279 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 220 GLN B 340 ASN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9148 Z= 0.247 Angle : 0.546 14.612 12380 Z= 0.279 Chirality : 0.041 0.180 1408 Planarity : 0.004 0.064 1540 Dihedral : 5.191 57.229 1288 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.52 % Allowed : 26.89 % Favored : 67.59 % 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: 0.83 (0.25), residues: 1114 helix: 2.44 (0.24), residues: 424 sheet: -0.62 (0.29), residues: 280 loop : -0.54 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 98 HIS 0.003 0.001 HIS A 213 PHE 0.012 0.001 PHE R 106 TYR 0.025 0.001 TYR S 223 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 237 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7174 (tp30) cc_final: 0.6887 (tp30) REVERT: A 184 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8331 (tt) REVERT: A 192 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8046 (mptm) REVERT: A 231 ASP cc_start: 0.7713 (t0) cc_final: 0.7347 (t0) REVERT: A 275 GLU cc_start: 0.7371 (tp30) cc_final: 0.7078 (tp30) REVERT: A 289 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7062 (tm-30) REVERT: B 19 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.7164 (ttm-80) REVERT: B 32 GLN cc_start: 0.8366 (mt0) cc_final: 0.8047 (mt0) REVERT: B 35 ASN cc_start: 0.7983 (t0) cc_final: 0.7622 (t0) REVERT: B 37 ILE cc_start: 0.8760 (tt) cc_final: 0.8383 (pt) REVERT: B 68 ARG cc_start: 0.8761 (ttt-90) cc_final: 0.8386 (tpp80) REVERT: B 177 THR cc_start: 0.8481 (m) cc_final: 0.8278 (t) REVERT: B 217 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7793 (ppp) REVERT: S 142 SER cc_start: 0.8278 (m) cc_final: 0.8039 (p) REVERT: S 234 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6464 (mp0) REVERT: R 76 PHE cc_start: 0.6305 (OUTLIER) cc_final: 0.5811 (m-80) REVERT: R 143 LEU cc_start: 0.8164 (tm) cc_final: 0.7959 (tt) outliers start: 54 outliers final: 34 residues processed: 265 average time/residue: 1.1169 time to fit residues: 316.0988 Evaluate side-chains 276 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 237 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 281 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 99 optimal weight: 0.0370 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 340 ASN S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9148 Z= 0.200 Angle : 0.541 14.522 12380 Z= 0.277 Chirality : 0.041 0.165 1408 Planarity : 0.004 0.071 1540 Dihedral : 5.116 55.299 1288 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.91 % Allowed : 27.81 % Favored : 67.28 % 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: 0.87 (0.26), residues: 1114 helix: 2.47 (0.24), residues: 425 sheet: -0.59 (0.29), residues: 283 loop : -0.53 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 98 HIS 0.003 0.001 HIS R 276 PHE 0.014 0.001 PHE R 72 TYR 0.024 0.001 TYR S 223 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 236 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7273 (tp30) cc_final: 0.6979 (tp30) REVERT: A 184 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8334 (tt) REVERT: A 192 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7957 (mptm) REVERT: A 231 ASP cc_start: 0.7703 (t0) cc_final: 0.7328 (t0) REVERT: A 275 GLU cc_start: 0.7361 (tp30) cc_final: 0.7087 (tp30) REVERT: A 289 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7053 (tm-30) REVERT: B 19 ARG cc_start: 0.7460 (ttm-80) cc_final: 0.7151 (ttm-80) REVERT: B 32 GLN cc_start: 0.8348 (mt0) cc_final: 0.8010 (mt0) REVERT: B 37 ILE cc_start: 0.8747 (tt) cc_final: 0.8376 (pt) REVERT: B 68 ARG cc_start: 0.8750 (ttt-90) cc_final: 0.8402 (tpp80) REVERT: B 170 ASP cc_start: 0.7873 (t0) cc_final: 0.7536 (t0) REVERT: B 234 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8488 (t80) REVERT: S 142 SER cc_start: 0.8266 (m) cc_final: 0.8025 (p) REVERT: S 234 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: R 76 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5559 (m-80) REVERT: R 143 LEU cc_start: 0.8130 (tm) cc_final: 0.7920 (tt) outliers start: 48 outliers final: 34 residues processed: 265 average time/residue: 1.1972 time to fit residues: 340.6542 Evaluate side-chains 273 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 234 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 281 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.0980 chunk 65 optimal weight: 0.0770 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 0.0570 overall best weight: 0.2256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 340 ASN S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9148 Z= 0.162 Angle : 0.525 13.683 12380 Z= 0.269 Chirality : 0.040 0.145 1408 Planarity : 0.004 0.077 1540 Dihedral : 4.958 52.023 1288 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.40 % Allowed : 28.43 % Favored : 67.18 % 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: 1.00 (0.26), residues: 1114 helix: 2.60 (0.24), residues: 425 sheet: -0.59 (0.30), residues: 285 loop : -0.44 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 98 HIS 0.003 0.001 HIS R 276 PHE 0.013 0.001 PHE R 72 TYR 0.020 0.001 TYR S 223 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 250 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7283 (tp30) cc_final: 0.6980 (tp30) REVERT: A 184 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8335 (tt) REVERT: A 231 ASP cc_start: 0.7657 (t0) cc_final: 0.7240 (t0) REVERT: A 275 GLU cc_start: 0.7339 (tp30) cc_final: 0.7049 (tp30) REVERT: A 289 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7029 (tm-30) REVERT: A 298 GLU cc_start: 0.7029 (tp30) cc_final: 0.6659 (tp30) REVERT: B 19 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.7123 (ttm-80) REVERT: B 32 GLN cc_start: 0.8268 (mt0) cc_final: 0.7920 (mt0) REVERT: B 37 ILE cc_start: 0.8709 (tt) cc_final: 0.8281 (pt) REVERT: B 59 TYR cc_start: 0.8286 (m-80) cc_final: 0.7816 (m-80) REVERT: B 68 ARG cc_start: 0.8703 (ttt-90) cc_final: 0.8385 (tpp80) REVERT: B 170 ASP cc_start: 0.7803 (t0) cc_final: 0.7552 (t0) REVERT: B 217 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7875 (ppp) REVERT: B 219 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.7839 (mtp85) REVERT: B 325 MET cc_start: 0.8244 (mtt) cc_final: 0.7637 (mtm) REVERT: S 234 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: R 76 PHE cc_start: 0.5999 (OUTLIER) cc_final: 0.5540 (m-80) REVERT: R 150 ILE cc_start: 0.7806 (mp) cc_final: 0.7422 (mm) outliers start: 43 outliers final: 30 residues processed: 275 average time/residue: 1.1397 time to fit residues: 334.5832 Evaluate side-chains 278 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 244 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 281 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 340 ASN S 77 ASN ** R 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 9148 Z= 0.262 Angle : 0.559 13.547 12380 Z= 0.285 Chirality : 0.042 0.158 1408 Planarity : 0.004 0.078 1540 Dihedral : 5.111 55.718 1288 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.99 % Allowed : 28.43 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1114 helix: 2.52 (0.24), residues: 425 sheet: -0.53 (0.30), residues: 280 loop : -0.49 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 213 PHE 0.016 0.002 PHE R 188 TYR 0.026 0.001 TYR S 223 ARG 0.010 0.001 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 238 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7192 (tp30) cc_final: 0.6892 (tp30) REVERT: A 184 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8326 (tt) REVERT: A 231 ASP cc_start: 0.7697 (t0) cc_final: 0.7263 (t0) REVERT: A 275 GLU cc_start: 0.7371 (tp30) cc_final: 0.7046 (tp30) REVERT: A 289 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7059 (tm-30) REVERT: B 19 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.7152 (ttm-80) REVERT: B 32 GLN cc_start: 0.8286 (mt0) cc_final: 0.7943 (mt0) REVERT: B 37 ILE cc_start: 0.8735 (tt) cc_final: 0.8289 (pt) REVERT: B 68 ARG cc_start: 0.8757 (ttt-90) cc_final: 0.8388 (tpp80) REVERT: B 170 ASP cc_start: 0.7821 (t0) cc_final: 0.7521 (t0) REVERT: B 217 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7838 (ppp) REVERT: B 219 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.7876 (mtp85) REVERT: B 254 ASP cc_start: 0.7475 (p0) cc_final: 0.7156 (p0) REVERT: S 234 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: R 76 PHE cc_start: 0.6058 (OUTLIER) cc_final: 0.5601 (m-80) REVERT: R 150 ILE cc_start: 0.7940 (mp) cc_final: 0.7547 (mm) outliers start: 39 outliers final: 24 residues processed: 261 average time/residue: 1.1538 time to fit residues: 321.0217 Evaluate side-chains 260 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 232 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 281 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 340 ASN S 77 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.133440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117589 restraints weight = 13138.098| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.92 r_work: 0.3467 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 9148 Z= 0.300 Angle : 0.585 13.309 12380 Z= 0.298 Chirality : 0.043 0.171 1408 Planarity : 0.004 0.075 1540 Dihedral : 5.225 59.922 1288 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.58 % Allowed : 28.83 % Favored : 67.59 % 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: 0.84 (0.25), residues: 1114 helix: 2.43 (0.24), residues: 425 sheet: -0.59 (0.30), residues: 279 loop : -0.54 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.002 PHE R 72 TYR 0.028 0.001 TYR S 223 ARG 0.006 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4971.43 seconds wall clock time: 87 minutes 9.53 seconds (5229.53 seconds total)