Starting phenix.real_space_refine on Wed Sep 17 10:59:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e82_47700/09_2025/9e82_47700_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e82_47700/09_2025/9e82_47700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e82_47700/09_2025/9e82_47700_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e82_47700/09_2025/9e82_47700_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e82_47700/09_2025/9e82_47700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e82_47700/09_2025/9e82_47700.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 42 5.16 5 C 5304 2.51 5 N 1358 2.21 5 O 1494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8200 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2693 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 313} Chain breaks: 2 Chain: "B" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 122 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "H" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1620 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain breaks: 3 Chain: "L" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1576 Classifications: {'peptide': 204} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "R" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2161 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.14, per 1000 atoms: 0.26 Number of scatterers: 8200 At special positions: 0 Unit cell: (82.2121, 100.13, 159.154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 2 15.00 O 1494 8.00 N 1358 7.00 C 5304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS R 117 " - pdb=" SG CYS R 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 424.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 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: 19 helices and 19 sheets defined 25.0% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.817A pdb=" N ASN A 280 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.805A pdb=" N LEU L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 188 Processing helix chain 'R' and resid 39 through 70 Processing helix chain 'R' and resid 81 through 106 removed outlier: 3.663A pdb=" N TRP R 92 " --> pdb=" O ILE R 88 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) Proline residue: R 98 - end of helix Processing helix chain 'R' and resid 113 through 146 removed outlier: 3.782A pdb=" N THR R 136 " --> pdb=" O ILE R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 182 removed outlier: 3.932A pdb=" N ARG R 162 " --> pdb=" O LYS R 158 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL R 163 " --> pdb=" O MET R 159 " (cutoff:3.500A) Proline residue: R 178 - end of helix removed outlier: 3.543A pdb=" N TYR R 182 " --> pdb=" O PRO R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 205 removed outlier: 3.784A pdb=" N ILE R 205 " --> pdb=" O GLU R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 207 No H-bonds generated for 'chain 'R' and resid 207 through 207' Processing helix chain 'R' and resid 208 through 219 Processing helix chain 'R' and resid 221 through 239 removed outlier: 3.918A pdb=" N ILE R 227 " --> pdb=" O VAL R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 280 removed outlier: 3.573A pdb=" N SER R 256 " --> pdb=" O LYS R 252 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP R 265 " --> pdb=" O PHE R 261 " (cutoff:3.500A) Proline residue: R 267 - end of helix Processing helix chain 'R' and resid 286 through 311 removed outlier: 3.543A pdb=" N HIS R 298 " --> pdb=" O PHE R 294 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS R 307 " --> pdb=" O LEU R 303 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS R 308 " --> pdb=" O SER R 304 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 314 No H-bonds generated for 'chain 'R' and resid 312 through 314' Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 116 removed outlier: 3.732A pdb=" N TPO R 341 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.978A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG A 62 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 53 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 188 Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209 removed outlier: 6.224A pdb=" N TYR A 208 " --> pdb=" O MET A 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 249 through 251 removed outlier: 6.601A pdb=" N LYS A 324 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE A 233 " --> pdb=" O LYS A 324 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS A 326 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE A 231 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A 328 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 249 through 251 removed outlier: 3.979A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 343 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA9, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.376A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN H 42 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR H 121 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.376A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN H 42 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 139 through 143 removed outlier: 6.017A pdb=" N TYR H 195 " --> pdb=" O ASP H 163 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS H 183 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 170 through 173 removed outlier: 4.514A pdb=" N TYR H 213 " --> pdb=" O VAL H 230 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL H 230 " --> pdb=" O TYR H 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 13 Processing sheet with id=AB5, first strand: chain 'L' and resid 20 through 25 Processing sheet with id=AB6, first strand: chain 'L' and resid 34 through 36 removed outlier: 3.757A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 49 through 50 Processing sheet with id=AB8, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.633A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 145 through 150 Processing sheet with id=AC1, first strand: chain 'R' and resid 183 through 187 375 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1366 1.32 - 1.45: 2251 1.45 - 1.57: 4728 1.57 - 1.69: 0 1.69 - 1.81: 57 Bond restraints: 8402 Sorted by residual: bond pdb=" CG HIS A 353 " pdb=" CD2 HIS A 353 " ideal model delta sigma weight residual 1.354 1.311 0.043 1.10e-02 8.26e+03 1.54e+01 bond pdb=" N VAL A 34 " pdb=" CA VAL A 34 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 8.91e+00 bond pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 1.469 1.431 0.037 1.28e-02 6.10e+03 8.49e+00 bond pdb=" C PRO A 36 " pdb=" O PRO A 36 " ideal model delta sigma weight residual 1.233 1.203 0.030 1.12e-02 7.97e+03 7.40e+00 bond pdb=" C HIS A 353 " pdb=" O HIS A 353 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.21e-02 6.83e+03 6.90e+00 ... (remaining 8397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 11190 1.51 - 3.02: 186 3.02 - 4.54: 48 4.54 - 6.05: 3 6.05 - 7.56: 2 Bond angle restraints: 11429 Sorted by residual: angle pdb=" C HIS A 353 " pdb=" CA HIS A 353 " pdb=" CB HIS A 353 " ideal model delta sigma weight residual 108.63 101.07 7.56 1.54e+00 4.22e-01 2.41e+01 angle pdb=" CB HIS A 353 " pdb=" CG HIS A 353 " pdb=" CD2 HIS A 353 " ideal model delta sigma weight residual 131.20 126.21 4.99 1.30e+00 5.92e-01 1.48e+01 angle pdb=" CA MET A 352 " pdb=" C MET A 352 " pdb=" O MET A 352 " ideal model delta sigma weight residual 120.51 115.05 5.46 1.43e+00 4.89e-01 1.46e+01 angle pdb=" N PRO A 36 " pdb=" CA PRO A 36 " pdb=" C PRO A 36 " ideal model delta sigma weight residual 111.68 118.03 -6.35 1.67e+00 3.59e-01 1.45e+01 angle pdb=" N PRO A 36 " pdb=" CA PRO A 36 " pdb=" CB PRO A 36 " ideal model delta sigma weight residual 103.15 99.65 3.50 9.70e-01 1.06e+00 1.30e+01 ... (remaining 11424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.35: 4712 13.35 - 26.70: 257 26.70 - 40.05: 59 40.05 - 53.40: 24 53.40 - 66.75: 8 Dihedral angle restraints: 5060 sinusoidal: 2017 harmonic: 3043 Sorted by residual: dihedral pdb=" CA TRP H 109 " pdb=" C TRP H 109 " pdb=" N GLY H 110 " pdb=" CA GLY H 110 " ideal model delta harmonic sigma weight residual -180.00 -154.31 -25.69 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" C HIS A 353 " pdb=" N HIS A 353 " pdb=" CA HIS A 353 " pdb=" CB HIS A 353 " ideal model delta harmonic sigma weight residual -122.60 -112.10 -10.50 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" CA VAL R 313 " pdb=" C VAL R 313 " pdb=" N LEU R 314 " pdb=" CA LEU R 314 " ideal model delta harmonic sigma weight residual 180.00 163.00 17.00 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 5057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 993 0.040 - 0.081: 212 0.081 - 0.121: 99 0.121 - 0.162: 12 0.162 - 0.202: 2 Chirality restraints: 1318 Sorted by residual: chirality pdb=" CA VAL A 34 " pdb=" N VAL A 34 " pdb=" C VAL A 34 " pdb=" CB VAL A 34 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA HIS A 353 " pdb=" N HIS A 353 " pdb=" C HIS A 353 " pdb=" CB HIS A 353 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CB VAL A 34 " pdb=" CA VAL A 34 " pdb=" CG1 VAL A 34 " pdb=" CG2 VAL A 34 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 1315 not shown) Planarity restraints: 1408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 258 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C VAL R 258 " -0.030 2.00e-02 2.50e+03 pdb=" O VAL R 258 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL R 259 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 352 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C MET A 352 " -0.029 2.00e-02 2.50e+03 pdb=" O MET A 352 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS A 353 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 167 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO H 168 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 168 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 168 " 0.020 5.00e-02 4.00e+02 ... (remaining 1405 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 157 2.63 - 3.20: 7746 3.20 - 3.77: 12299 3.77 - 4.33: 17258 4.33 - 4.90: 28411 Nonbonded interactions: 65871 Sorted by model distance: nonbonded pdb=" OG SER A 193 " pdb=" OD1 ASN A 225 " model vdw 2.068 3.040 nonbonded pdb=" O VAL H 32 " pdb=" OG SER H 56 " model vdw 2.074 3.040 nonbonded pdb=" OG SER L 160 " pdb=" OG SER L 178 " model vdw 2.104 3.040 nonbonded pdb=" O VAL L 30 " pdb=" NH2 ARG L 67 " model vdw 2.135 3.120 nonbonded pdb=" OH TYR L 37 " pdb=" OE1 GLN L 90 " model vdw 2.140 3.040 ... (remaining 65866 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: 4.290 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.610 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 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 0.043 8407 Z= 0.180 Angle : 0.529 7.559 11439 Z= 0.301 Chirality : 0.042 0.202 1318 Planarity : 0.004 0.040 1408 Dihedral : 9.814 66.753 3075 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.04 % Allowed : 5.86 % Favored : 91.10 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.28), residues: 997 helix: 1.45 (0.37), residues: 200 sheet: -0.83 (0.29), residues: 358 loop : -0.64 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 143 TYR 0.008 0.001 TYR L 94 PHE 0.009 0.001 PHE A 27 TRP 0.008 0.001 TRP H 50 HIS 0.004 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8402) covalent geometry : angle 0.52872 (11429) SS BOND : bond 0.00234 ( 5) SS BOND : angle 0.64746 ( 10) hydrogen bonds : bond 0.14274 ( 353) hydrogen bonds : angle 6.85870 ( 1023) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 298 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 PHE cc_start: 0.8443 (m-80) cc_final: 0.8187 (m-80) REVERT: A 17 LYS cc_start: 0.6370 (mttt) cc_final: 0.6144 (mttt) REVERT: A 58 THR cc_start: 0.7873 (m) cc_final: 0.7479 (p) REVERT: A 197 LEU cc_start: 0.5163 (OUTLIER) cc_final: 0.4603 (tp) REVERT: A 281 ASN cc_start: 0.8626 (m110) cc_final: 0.8377 (m-40) REVERT: A 314 ILE cc_start: 0.8287 (mp) cc_final: 0.7664 (mp) REVERT: H 8 VAL cc_start: 0.8134 (t) cc_final: 0.7851 (p) REVERT: H 61 THR cc_start: 0.8626 (p) cc_final: 0.8390 (p) REVERT: H 102 LYS cc_start: 0.7348 (tptt) cc_final: 0.7074 (tptt) REVERT: H 139 SER cc_start: 0.5606 (t) cc_final: 0.4756 (p) REVERT: H 162 LYS cc_start: 0.7270 (tttp) cc_final: 0.6603 (tttp) REVERT: H 228 LYS cc_start: 0.8364 (tptm) cc_final: 0.7865 (mttt) REVERT: L 12 LEU cc_start: 0.8663 (pp) cc_final: 0.8224 (pp) REVERT: L 48 LEU cc_start: 0.7330 (mt) cc_final: 0.7109 (mt) REVERT: L 56 TYR cc_start: 0.6873 (t80) cc_final: 0.6640 (t80) REVERT: L 72 PHE cc_start: 0.8557 (m-80) cc_final: 0.8079 (m-80) REVERT: L 106 GLU cc_start: 0.7298 (mp0) cc_final: 0.7061 (mp0) REVERT: L 164 VAL cc_start: 0.8415 (t) cc_final: 0.8118 (p) REVERT: R 298 HIS cc_start: 0.7977 (m-70) cc_final: 0.7760 (m-70) outliers start: 28 outliers final: 15 residues processed: 316 average time/residue: 0.0995 time to fit residues: 42.5767 Evaluate side-chains 272 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 256 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN B 2 HIS H 31 ASN H 190 GLN L 80 GLN L 125 GLN R 191 ASN R 291 HIS R 321 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.228879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.179704 restraints weight = 12852.640| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 4.21 r_work: 0.3881 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8407 Z= 0.229 Angle : 0.706 8.734 11439 Z= 0.367 Chirality : 0.047 0.165 1318 Planarity : 0.006 0.082 1408 Dihedral : 6.862 54.756 1211 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.13 % Allowed : 12.70 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.28), residues: 997 helix: 1.02 (0.34), residues: 207 sheet: -0.84 (0.28), residues: 356 loop : -0.51 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 282 TYR 0.020 0.002 TYR L 141 PHE 0.027 0.002 PHE R 173 TRP 0.024 0.002 TRP L 36 HIS 0.006 0.001 HIS H 219 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 8402) covalent geometry : angle 0.70570 (11429) SS BOND : bond 0.00233 ( 5) SS BOND : angle 1.10701 ( 10) hydrogen bonds : bond 0.04382 ( 353) hydrogen bonds : angle 5.97395 ( 1023) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 262 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8591 (mtm110) cc_final: 0.8054 (ttp-110) REVERT: A 9 PHE cc_start: 0.8720 (m-80) cc_final: 0.8365 (m-80) REVERT: A 58 THR cc_start: 0.8207 (m) cc_final: 0.7791 (p) REVERT: A 87 PHE cc_start: 0.8380 (t80) cc_final: 0.8016 (t80) REVERT: A 122 ASN cc_start: 0.7823 (t0) cc_final: 0.6686 (t0) REVERT: A 130 GLN cc_start: 0.7076 (tt0) cc_final: 0.6875 (tt0) REVERT: A 197 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5351 (tp) REVERT: H 90 ARG cc_start: 0.7534 (mpp80) cc_final: 0.7282 (mpt-90) REVERT: H 102 LYS cc_start: 0.7500 (tptt) cc_final: 0.7090 (tptm) REVERT: H 106 HIS cc_start: 0.7680 (t70) cc_final: 0.7453 (t70) REVERT: H 139 SER cc_start: 0.5677 (t) cc_final: 0.4935 (p) REVERT: H 162 LYS cc_start: 0.7561 (tttp) cc_final: 0.6834 (tttp) REVERT: H 190 GLN cc_start: 0.7911 (tp-100) cc_final: 0.7675 (tp40) REVERT: H 228 LYS cc_start: 0.8254 (tptm) cc_final: 0.7842 (mttt) REVERT: L 28 GLN cc_start: 0.7692 (mp10) cc_final: 0.7407 (mm110) REVERT: L 48 LEU cc_start: 0.7656 (mt) cc_final: 0.7437 (mm) REVERT: L 56 TYR cc_start: 0.7357 (t80) cc_final: 0.6967 (t80) REVERT: L 71 ASP cc_start: 0.8113 (t0) cc_final: 0.7888 (t0) REVERT: L 86 THR cc_start: 0.7615 (OUTLIER) cc_final: 0.7193 (m) REVERT: L 105 VAL cc_start: 0.8289 (t) cc_final: 0.7702 (p) REVERT: L 164 VAL cc_start: 0.8485 (t) cc_final: 0.7312 (p) REVERT: R 277 PHE cc_start: 0.7167 (t80) cc_final: 0.6878 (t80) REVERT: R 298 HIS cc_start: 0.8665 (m-70) cc_final: 0.8238 (m-70) REVERT: R 340 LEU cc_start: 0.8855 (mt) cc_final: 0.7500 (pp) REVERT: R 342 LYS cc_start: 0.8411 (tmtt) cc_final: 0.8139 (tptp) outliers start: 38 outliers final: 25 residues processed: 284 average time/residue: 0.0984 time to fit residues: 37.8220 Evaluate side-chains 277 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 250 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 253 ILE Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 0.4980 chunk 74 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 76 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 HIS L 7 GLN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 ASN ** R 127 ASN ** 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 = 0.4675 r_free = 0.4675 target = 0.232263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.183216 restraints weight = 12826.214| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 4.17 r_work: 0.3901 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8407 Z= 0.189 Angle : 0.682 7.749 11439 Z= 0.352 Chirality : 0.046 0.154 1318 Planarity : 0.006 0.086 1408 Dihedral : 6.836 57.742 1205 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.23 % Allowed : 15.85 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.28), residues: 997 helix: 0.93 (0.35), residues: 202 sheet: -0.70 (0.28), residues: 358 loop : -0.45 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 312 TYR 0.027 0.002 TYR L 141 PHE 0.032 0.002 PHE R 173 TRP 0.030 0.002 TRP H 39 HIS 0.028 0.002 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8402) covalent geometry : angle 0.67936 (11429) SS BOND : bond 0.00237 ( 5) SS BOND : angle 1.98725 ( 10) hydrogen bonds : bond 0.04071 ( 353) hydrogen bonds : angle 5.91665 ( 1023) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 255 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8559 (mtm110) cc_final: 0.7992 (ttp-110) REVERT: A 9 PHE cc_start: 0.8672 (m-80) cc_final: 0.8313 (m-80) REVERT: A 17 LYS cc_start: 0.7426 (mmmt) cc_final: 0.7042 (mmtt) REVERT: A 19 THR cc_start: 0.5630 (OUTLIER) cc_final: 0.5124 (p) REVERT: A 58 THR cc_start: 0.8214 (m) cc_final: 0.7784 (p) REVERT: A 122 ASN cc_start: 0.7813 (t0) cc_final: 0.6475 (t0) REVERT: A 130 GLN cc_start: 0.6953 (tt0) cc_final: 0.6554 (tt0) REVERT: H 102 LYS cc_start: 0.7485 (tptt) cc_final: 0.6876 (tptm) REVERT: H 112 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7503 (mt) REVERT: H 129 THR cc_start: 0.8311 (m) cc_final: 0.8058 (p) REVERT: H 162 LYS cc_start: 0.7522 (tttp) cc_final: 0.7020 (tttp) REVERT: H 190 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7779 (tp40) REVERT: L 28 GLN cc_start: 0.7869 (mp10) cc_final: 0.7645 (mm110) REVERT: L 48 LEU cc_start: 0.7790 (mt) cc_final: 0.7535 (mm) REVERT: L 50 TYR cc_start: 0.8495 (p90) cc_final: 0.7918 (p90) REVERT: L 56 TYR cc_start: 0.7369 (t80) cc_final: 0.7052 (t80) REVERT: L 59 VAL cc_start: 0.8593 (m) cc_final: 0.8315 (p) REVERT: L 71 ASP cc_start: 0.8083 (t0) cc_final: 0.7772 (t0) REVERT: L 105 VAL cc_start: 0.8243 (t) cc_final: 0.7548 (p) REVERT: L 143 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7627 (ttm-80) REVERT: R 277 PHE cc_start: 0.7080 (t80) cc_final: 0.6743 (t80) REVERT: R 298 HIS cc_start: 0.8703 (m-70) cc_final: 0.8261 (m-70) REVERT: R 340 LEU cc_start: 0.8856 (mt) cc_final: 0.7309 (pp) outliers start: 39 outliers final: 26 residues processed: 277 average time/residue: 0.1017 time to fit residues: 38.0655 Evaluate side-chains 270 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 242 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 85 ASN Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 253 ILE Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 8 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 46 optimal weight: 0.0670 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 11 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.234138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.185193 restraints weight = 13142.250| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 4.26 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8407 Z= 0.151 Angle : 0.663 7.677 11439 Z= 0.344 Chirality : 0.046 0.182 1318 Planarity : 0.006 0.095 1408 Dihedral : 6.744 59.698 1201 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.13 % Allowed : 16.61 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.27), residues: 997 helix: 0.78 (0.35), residues: 203 sheet: -0.44 (0.29), residues: 347 loop : -0.56 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 22 TYR 0.028 0.001 TYR L 141 PHE 0.023 0.002 PHE L 140 TRP 0.034 0.002 TRP H 39 HIS 0.016 0.002 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8402) covalent geometry : angle 0.66156 (11429) SS BOND : bond 0.00439 ( 5) SS BOND : angle 1.68637 ( 10) hydrogen bonds : bond 0.03931 ( 353) hydrogen bonds : angle 5.72139 ( 1023) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8381 (mtm110) cc_final: 0.7897 (ttp-110) REVERT: A 9 PHE cc_start: 0.8528 (m-80) cc_final: 0.8166 (m-80) REVERT: A 17 LYS cc_start: 0.7117 (mmmt) cc_final: 0.6888 (mmtt) REVERT: A 19 THR cc_start: 0.5576 (OUTLIER) cc_final: 0.5116 (p) REVERT: A 58 THR cc_start: 0.7793 (m) cc_final: 0.7477 (p) REVERT: A 104 LEU cc_start: -0.0714 (OUTLIER) cc_final: -0.1261 (mt) REVERT: A 169 ARG cc_start: 0.7556 (mtm180) cc_final: 0.6548 (mtm180) REVERT: H 5 VAL cc_start: 0.8250 (t) cc_final: 0.7259 (t) REVERT: H 102 LYS cc_start: 0.7151 (tptt) cc_final: 0.6633 (tptm) REVERT: H 112 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6836 (mt) REVERT: H 129 THR cc_start: 0.7920 (m) cc_final: 0.7687 (p) REVERT: H 190 GLN cc_start: 0.7963 (tp-100) cc_final: 0.7724 (tp40) REVERT: H 228 LYS cc_start: 0.8192 (tptm) cc_final: 0.7891 (tttt) REVERT: L 28 GLN cc_start: 0.7709 (mp10) cc_final: 0.7498 (mm110) REVERT: L 50 TYR cc_start: 0.8078 (p90) cc_final: 0.7486 (p90) REVERT: L 56 TYR cc_start: 0.7063 (t80) cc_final: 0.6785 (t80) REVERT: L 71 ASP cc_start: 0.8077 (t0) cc_final: 0.7739 (t0) REVERT: L 105 VAL cc_start: 0.8029 (OUTLIER) cc_final: 0.6916 (p) REVERT: L 193 TYR cc_start: 0.4971 (m-80) cc_final: 0.4735 (m-80) REVERT: R 277 PHE cc_start: 0.7060 (t80) cc_final: 0.6722 (t80) REVERT: R 298 HIS cc_start: 0.8189 (m-70) cc_final: 0.7768 (m-70) REVERT: R 320 ARG cc_start: 0.7874 (ttm170) cc_final: 0.7613 (ttm-80) REVERT: R 340 LEU cc_start: 0.8780 (mt) cc_final: 0.7200 (pp) outliers start: 38 outliers final: 28 residues processed: 265 average time/residue: 0.0947 time to fit residues: 34.5293 Evaluate side-chains 270 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 253 ILE Chi-restraints excluded: chain R residue 309 CYS Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 321 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 80 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.233196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.183049 restraints weight = 13012.870| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 4.39 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8407 Z= 0.181 Angle : 0.669 7.755 11439 Z= 0.347 Chirality : 0.046 0.227 1318 Planarity : 0.006 0.079 1408 Dihedral : 6.758 59.712 1201 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.89 % Allowed : 18.13 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.27), residues: 997 helix: 0.73 (0.34), residues: 203 sheet: -0.37 (0.29), residues: 347 loop : -0.62 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 143 TYR 0.021 0.001 TYR L 93 PHE 0.024 0.002 PHE L 140 TRP 0.030 0.002 TRP L 36 HIS 0.017 0.002 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8402) covalent geometry : angle 0.66758 (11429) SS BOND : bond 0.00211 ( 5) SS BOND : angle 1.59535 ( 10) hydrogen bonds : bond 0.03887 ( 353) hydrogen bonds : angle 5.75990 ( 1023) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8476 (mtm110) cc_final: 0.7916 (ttp-110) REVERT: A 9 PHE cc_start: 0.8596 (m-80) cc_final: 0.8217 (m-80) REVERT: A 17 LYS cc_start: 0.7070 (mmmt) cc_final: 0.6840 (mmtt) REVERT: A 19 THR cc_start: 0.5605 (OUTLIER) cc_final: 0.5144 (p) REVERT: A 58 THR cc_start: 0.7846 (m) cc_final: 0.7534 (p) REVERT: A 104 LEU cc_start: -0.1008 (OUTLIER) cc_final: -0.1528 (mt) REVERT: A 169 ARG cc_start: 0.7546 (mtm180) cc_final: 0.6524 (mtm180) REVERT: H 102 LYS cc_start: 0.7354 (tptt) cc_final: 0.6771 (tptm) REVERT: H 112 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6965 (mt) REVERT: H 129 THR cc_start: 0.7893 (m) cc_final: 0.7621 (p) REVERT: H 190 GLN cc_start: 0.7934 (tp-100) cc_final: 0.7723 (tp40) REVERT: H 228 LYS cc_start: 0.8203 (tptm) cc_final: 0.7879 (tttt) REVERT: L 4 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7640 (tm-30) REVERT: L 28 GLN cc_start: 0.7827 (mp10) cc_final: 0.7544 (mm110) REVERT: L 50 TYR cc_start: 0.8076 (p90) cc_final: 0.7487 (p90) REVERT: L 56 TYR cc_start: 0.6926 (t80) cc_final: 0.6669 (t80) REVERT: L 71 ASP cc_start: 0.8166 (t0) cc_final: 0.7759 (t0) REVERT: L 105 VAL cc_start: 0.7805 (t) cc_final: 0.6752 (p) REVERT: R 48 SER cc_start: 0.8743 (m) cc_final: 0.8533 (p) REVERT: R 49 PHE cc_start: 0.8289 (m-80) cc_final: 0.8041 (m-80) REVERT: R 277 PHE cc_start: 0.7229 (t80) cc_final: 0.6843 (t80) REVERT: R 298 HIS cc_start: 0.8252 (m-70) cc_final: 0.7810 (m-70) REVERT: R 320 ARG cc_start: 0.7810 (ttm170) cc_final: 0.7524 (ttm-80) REVERT: R 340 LEU cc_start: 0.8798 (mt) cc_final: 0.7230 (pp) outliers start: 45 outliers final: 36 residues processed: 267 average time/residue: 0.0919 time to fit residues: 33.7564 Evaluate side-chains 279 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 253 ILE Chi-restraints excluded: chain R residue 309 CYS Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 75 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 30 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.232219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.182599 restraints weight = 12916.806| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 4.27 r_work: 0.3930 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8407 Z= 0.159 Angle : 0.666 8.088 11439 Z= 0.346 Chirality : 0.046 0.220 1318 Planarity : 0.006 0.065 1408 Dihedral : 6.737 59.411 1201 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.99 % Allowed : 19.33 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.27), residues: 997 helix: 0.62 (0.34), residues: 207 sheet: -0.33 (0.29), residues: 348 loop : -0.62 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 143 TYR 0.021 0.001 TYR L 93 PHE 0.035 0.002 PHE R 173 TRP 0.044 0.003 TRP L 36 HIS 0.017 0.002 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8402) covalent geometry : angle 0.66494 (11429) SS BOND : bond 0.00207 ( 5) SS BOND : angle 1.33651 ( 10) hydrogen bonds : bond 0.03805 ( 353) hydrogen bonds : angle 5.73216 ( 1023) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8535 (mtm110) cc_final: 0.7975 (ttp-110) REVERT: A 9 PHE cc_start: 0.8688 (m-80) cc_final: 0.8303 (m-80) REVERT: A 17 LYS cc_start: 0.7144 (mmmt) cc_final: 0.6886 (mmtt) REVERT: A 19 THR cc_start: 0.5636 (OUTLIER) cc_final: 0.5147 (p) REVERT: A 58 THR cc_start: 0.8053 (m) cc_final: 0.7678 (p) REVERT: A 104 LEU cc_start: -0.0606 (OUTLIER) cc_final: -0.1262 (mt) REVERT: A 169 ARG cc_start: 0.7756 (mtm180) cc_final: 0.6964 (mtm180) REVERT: H 90 ARG cc_start: 0.7645 (mpt-90) cc_final: 0.7328 (mmt90) REVERT: H 102 LYS cc_start: 0.7414 (tptt) cc_final: 0.7031 (tptm) REVERT: H 112 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7627 (mt) REVERT: H 124 GLN cc_start: 0.8128 (pp30) cc_final: 0.7887 (pp30) REVERT: H 129 THR cc_start: 0.8233 (m) cc_final: 0.7971 (p) REVERT: H 190 GLN cc_start: 0.8029 (tp-100) cc_final: 0.7769 (tp40) REVERT: L 28 GLN cc_start: 0.7932 (mp10) cc_final: 0.7662 (mm110) REVERT: L 38 GLN cc_start: 0.7933 (tt0) cc_final: 0.7496 (tm-30) REVERT: L 50 TYR cc_start: 0.8457 (p90) cc_final: 0.7949 (p90) REVERT: L 56 TYR cc_start: 0.7159 (t80) cc_final: 0.6731 (t80) REVERT: L 71 ASP cc_start: 0.8171 (t0) cc_final: 0.7741 (t0) REVERT: L 143 ARG cc_start: 0.8375 (ttm110) cc_final: 0.8047 (ttm110) REVERT: R 49 PHE cc_start: 0.8355 (m-80) cc_final: 0.8059 (m-80) REVERT: R 277 PHE cc_start: 0.7234 (t80) cc_final: 0.6849 (t80) REVERT: R 298 HIS cc_start: 0.8656 (m-70) cc_final: 0.8188 (m-70) REVERT: R 320 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7552 (ttm-80) REVERT: R 340 LEU cc_start: 0.8856 (mt) cc_final: 0.7340 (pp) outliers start: 46 outliers final: 37 residues processed: 262 average time/residue: 0.0909 time to fit residues: 32.6441 Evaluate side-chains 272 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 253 ILE Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 309 CYS Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 84 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 311 ASN R 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.229105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.183772 restraints weight = 12987.719| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 3.89 r_work: 0.3894 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 8407 Z= 0.242 Angle : 0.706 8.255 11439 Z= 0.372 Chirality : 0.048 0.256 1318 Planarity : 0.006 0.070 1408 Dihedral : 6.899 59.874 1201 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.10 % Allowed : 19.87 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.27), residues: 997 helix: 0.39 (0.34), residues: 208 sheet: -0.36 (0.29), residues: 341 loop : -0.77 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 143 TYR 0.024 0.002 TYR L 93 PHE 0.033 0.002 PHE R 173 TRP 0.071 0.003 TRP L 36 HIS 0.010 0.002 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 8402) covalent geometry : angle 0.70337 (11429) SS BOND : bond 0.00245 ( 5) SS BOND : angle 2.08475 ( 10) hydrogen bonds : bond 0.04138 ( 353) hydrogen bonds : angle 5.97008 ( 1023) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8558 (mtm110) cc_final: 0.8012 (ttp-110) REVERT: A 9 PHE cc_start: 0.8750 (m-80) cc_final: 0.8301 (m-80) REVERT: A 17 LYS cc_start: 0.7240 (mmmt) cc_final: 0.6965 (mmtt) REVERT: A 19 THR cc_start: 0.5693 (OUTLIER) cc_final: 0.5203 (p) REVERT: A 58 THR cc_start: 0.8245 (m) cc_final: 0.7836 (p) REVERT: A 104 LEU cc_start: -0.0667 (OUTLIER) cc_final: -0.0877 (tp) REVERT: A 169 ARG cc_start: 0.7826 (mtm180) cc_final: 0.6878 (mtm180) REVERT: A 292 LYS cc_start: 0.7925 (tttt) cc_final: 0.7666 (tttm) REVERT: A 294 LYS cc_start: 0.8674 (tptp) cc_final: 0.8458 (tptp) REVERT: H 22 ARG cc_start: 0.8118 (tmt170) cc_final: 0.7887 (tmt170) REVERT: H 90 ARG cc_start: 0.7803 (mpt-90) cc_final: 0.7529 (mmt90) REVERT: H 102 LYS cc_start: 0.7636 (tptt) cc_final: 0.7204 (tptm) REVERT: H 129 THR cc_start: 0.8260 (m) cc_final: 0.7983 (p) REVERT: H 190 GLN cc_start: 0.8074 (tp-100) cc_final: 0.7845 (tp40) REVERT: H 195 TYR cc_start: 0.8704 (m-80) cc_final: 0.8060 (m-10) REVERT: L 28 GLN cc_start: 0.7856 (mp10) cc_final: 0.7631 (mm110) REVERT: L 38 GLN cc_start: 0.7915 (tt0) cc_final: 0.7468 (tm-30) REVERT: L 50 TYR cc_start: 0.8533 (p90) cc_final: 0.7939 (p90) REVERT: L 56 TYR cc_start: 0.7167 (t80) cc_final: 0.6779 (t80) REVERT: L 71 ASP cc_start: 0.8179 (t0) cc_final: 0.7678 (t0) REVERT: L 143 ARG cc_start: 0.8296 (ttm110) cc_final: 0.7948 (ttm110) REVERT: R 277 PHE cc_start: 0.7300 (t80) cc_final: 0.6922 (t80) REVERT: R 298 HIS cc_start: 0.8675 (m-70) cc_final: 0.8203 (m-70) REVERT: R 320 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7714 (ttm-80) REVERT: R 340 LEU cc_start: 0.8873 (mt) cc_final: 0.7399 (pp) outliers start: 47 outliers final: 37 residues processed: 269 average time/residue: 0.0880 time to fit residues: 33.2212 Evaluate side-chains 276 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 237 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 253 ILE Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 309 CYS Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 83 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 GLN ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.229991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.180930 restraints weight = 12853.649| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 4.14 r_work: 0.3921 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8407 Z= 0.205 Angle : 0.717 14.436 11439 Z= 0.371 Chirality : 0.047 0.226 1318 Planarity : 0.006 0.069 1408 Dihedral : 6.856 59.522 1201 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 5.10 % Allowed : 21.93 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.27), residues: 997 helix: 0.29 (0.34), residues: 214 sheet: -0.36 (0.29), residues: 340 loop : -0.73 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 143 TYR 0.023 0.001 TYR L 93 PHE 0.034 0.002 PHE R 173 TRP 0.079 0.003 TRP L 36 HIS 0.009 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 8402) covalent geometry : angle 0.71451 (11429) SS BOND : bond 0.00426 ( 5) SS BOND : angle 2.08096 ( 10) hydrogen bonds : bond 0.04000 ( 353) hydrogen bonds : angle 5.95934 ( 1023) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 234 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8568 (mtm110) cc_final: 0.7944 (ttp-110) REVERT: A 9 PHE cc_start: 0.8725 (m-80) cc_final: 0.8314 (m-80) REVERT: A 17 LYS cc_start: 0.7251 (mmmt) cc_final: 0.6982 (mmtt) REVERT: A 19 THR cc_start: 0.5684 (OUTLIER) cc_final: 0.4995 (t) REVERT: A 58 THR cc_start: 0.8210 (m) cc_final: 0.7760 (p) REVERT: A 104 LEU cc_start: -0.0922 (OUTLIER) cc_final: -0.1201 (tp) REVERT: A 169 ARG cc_start: 0.7817 (mtm180) cc_final: 0.6970 (mtm180) REVERT: H 22 ARG cc_start: 0.8240 (tmt170) cc_final: 0.8009 (tmt170) REVERT: H 90 ARG cc_start: 0.7835 (mpt-90) cc_final: 0.7525 (mmt90) REVERT: H 102 LYS cc_start: 0.7540 (tptt) cc_final: 0.7098 (tptm) REVERT: H 129 THR cc_start: 0.8223 (m) cc_final: 0.7922 (p) REVERT: H 136 LYS cc_start: 0.6422 (mtpp) cc_final: 0.6216 (mtmt) REVERT: H 190 GLN cc_start: 0.8098 (tp-100) cc_final: 0.7861 (tp40) REVERT: H 195 TYR cc_start: 0.8650 (m-80) cc_final: 0.7959 (m-10) REVERT: H 228 LYS cc_start: 0.8396 (tptm) cc_final: 0.7981 (tttt) REVERT: L 28 GLN cc_start: 0.7869 (mp10) cc_final: 0.7636 (mm110) REVERT: L 38 GLN cc_start: 0.7911 (tt0) cc_final: 0.7407 (tm-30) REVERT: L 50 TYR cc_start: 0.8467 (p90) cc_final: 0.7858 (p90) REVERT: L 56 TYR cc_start: 0.7245 (t80) cc_final: 0.6841 (t80) REVERT: L 71 ASP cc_start: 0.7903 (t0) cc_final: 0.7515 (t0) REVERT: R 100 TRP cc_start: 0.7763 (m100) cc_final: 0.7085 (m100) REVERT: R 277 PHE cc_start: 0.7325 (t80) cc_final: 0.6928 (t80) REVERT: R 298 HIS cc_start: 0.8735 (m-70) cc_final: 0.8250 (m-70) REVERT: R 320 ARG cc_start: 0.7982 (ttm170) cc_final: 0.7769 (ttm-80) REVERT: R 340 LEU cc_start: 0.8893 (mt) cc_final: 0.7341 (pp) outliers start: 47 outliers final: 39 residues processed: 259 average time/residue: 0.0932 time to fit residues: 33.3511 Evaluate side-chains 272 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 36 TRP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 309 CYS Chi-restraints excluded: chain R residue 311 ASN Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 317 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 63 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.231215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.182335 restraints weight = 12876.326| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 4.20 r_work: 0.3920 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8407 Z= 0.185 Angle : 0.736 16.329 11439 Z= 0.378 Chirality : 0.047 0.210 1318 Planarity : 0.006 0.071 1408 Dihedral : 6.678 58.887 1200 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.56 % Allowed : 22.69 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.27), residues: 997 helix: 0.24 (0.33), residues: 214 sheet: -0.18 (0.30), residues: 334 loop : -0.80 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 312 TYR 0.023 0.001 TYR L 93 PHE 0.027 0.002 PHE L 140 TRP 0.082 0.003 TRP L 36 HIS 0.009 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 8402) covalent geometry : angle 0.73412 (11429) SS BOND : bond 0.00302 ( 5) SS BOND : angle 2.12492 ( 10) hydrogen bonds : bond 0.03937 ( 353) hydrogen bonds : angle 5.90449 ( 1023) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 PHE cc_start: 0.8735 (m-80) cc_final: 0.8371 (m-80) REVERT: A 17 LYS cc_start: 0.7250 (mmmt) cc_final: 0.7012 (mmtt) REVERT: A 19 THR cc_start: 0.5671 (OUTLIER) cc_final: 0.4980 (t) REVERT: A 58 THR cc_start: 0.8210 (m) cc_final: 0.7749 (p) REVERT: A 104 LEU cc_start: -0.0849 (OUTLIER) cc_final: -0.1633 (mt) REVERT: A 169 ARG cc_start: 0.7779 (mtm180) cc_final: 0.6914 (mtm180) REVERT: H 22 ARG cc_start: 0.8222 (tmt170) cc_final: 0.7938 (tmt170) REVERT: H 90 ARG cc_start: 0.7873 (mpt-90) cc_final: 0.7593 (mmt90) REVERT: H 102 LYS cc_start: 0.7458 (tptt) cc_final: 0.7025 (tptm) REVERT: H 129 THR cc_start: 0.8241 (m) cc_final: 0.7956 (p) REVERT: H 190 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7865 (tp40) REVERT: H 228 LYS cc_start: 0.8406 (tptm) cc_final: 0.8000 (tttt) REVERT: L 28 GLN cc_start: 0.7893 (mp10) cc_final: 0.7628 (mm110) REVERT: L 38 GLN cc_start: 0.8010 (tt0) cc_final: 0.7552 (tm-30) REVERT: L 50 TYR cc_start: 0.8506 (p90) cc_final: 0.7945 (p90) REVERT: L 56 TYR cc_start: 0.7205 (t80) cc_final: 0.6810 (t80) REVERT: L 71 ASP cc_start: 0.7890 (t0) cc_final: 0.7524 (t0) REVERT: L 143 ARG cc_start: 0.8721 (tpp80) cc_final: 0.8253 (tpp80) REVERT: R 277 PHE cc_start: 0.7385 (t80) cc_final: 0.6987 (t80) REVERT: R 298 HIS cc_start: 0.8690 (m-70) cc_final: 0.8203 (m-70) REVERT: R 340 LEU cc_start: 0.8906 (mt) cc_final: 0.7286 (pt) outliers start: 42 outliers final: 36 residues processed: 252 average time/residue: 0.0907 time to fit residues: 31.8174 Evaluate side-chains 264 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 36 TRP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 253 ILE Chi-restraints excluded: chain R residue 309 CYS Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 317 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 7 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 56 optimal weight: 0.0170 chunk 28 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.231686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.182522 restraints weight = 12801.241| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 4.21 r_work: 0.3915 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8407 Z= 0.181 Angle : 0.727 13.595 11439 Z= 0.377 Chirality : 0.047 0.292 1318 Planarity : 0.006 0.073 1408 Dihedral : 6.752 59.320 1200 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.45 % Allowed : 22.80 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.27), residues: 997 helix: 0.21 (0.34), residues: 214 sheet: -0.19 (0.30), residues: 334 loop : -0.77 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 312 TYR 0.023 0.001 TYR L 93 PHE 0.035 0.002 PHE R 173 TRP 0.079 0.003 TRP L 36 HIS 0.009 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 8402) covalent geometry : angle 0.72490 (11429) SS BOND : bond 0.00275 ( 5) SS BOND : angle 2.19205 ( 10) hydrogen bonds : bond 0.03939 ( 353) hydrogen bonds : angle 5.87332 ( 1023) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 PHE cc_start: 0.8699 (m-80) cc_final: 0.8361 (m-80) REVERT: A 17 LYS cc_start: 0.7250 (mmmt) cc_final: 0.7003 (mmtt) REVERT: A 19 THR cc_start: 0.5689 (OUTLIER) cc_final: 0.5003 (t) REVERT: A 58 THR cc_start: 0.8204 (m) cc_final: 0.7744 (p) REVERT: A 104 LEU cc_start: -0.0747 (OUTLIER) cc_final: -0.1570 (mt) REVERT: A 169 ARG cc_start: 0.7770 (mtm180) cc_final: 0.6920 (mtm180) REVERT: H 22 ARG cc_start: 0.8200 (tmt170) cc_final: 0.7988 (tmt170) REVERT: H 90 ARG cc_start: 0.7907 (mpt-90) cc_final: 0.7641 (mmt90) REVERT: H 102 LYS cc_start: 0.7435 (tptt) cc_final: 0.7003 (tptm) REVERT: H 129 THR cc_start: 0.8249 (m) cc_final: 0.7970 (p) REVERT: H 190 GLN cc_start: 0.8128 (tp-100) cc_final: 0.7882 (tp40) REVERT: H 195 TYR cc_start: 0.8734 (m-80) cc_final: 0.8078 (m-10) REVERT: H 228 LYS cc_start: 0.8411 (tptm) cc_final: 0.7975 (tttt) REVERT: L 4 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7793 (tm-30) REVERT: L 28 GLN cc_start: 0.7934 (mp10) cc_final: 0.7655 (mm110) REVERT: L 38 GLN cc_start: 0.8047 (tt0) cc_final: 0.7670 (tm-30) REVERT: L 50 TYR cc_start: 0.8460 (p90) cc_final: 0.7927 (p90) REVERT: L 56 TYR cc_start: 0.7207 (t80) cc_final: 0.6795 (t80) REVERT: L 71 ASP cc_start: 0.7896 (t0) cc_final: 0.7546 (t0) REVERT: L 143 ARG cc_start: 0.8724 (tpp80) cc_final: 0.8271 (tpp80) REVERT: R 55 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7697 (p90) REVERT: R 277 PHE cc_start: 0.7408 (t80) cc_final: 0.7036 (t80) REVERT: R 298 HIS cc_start: 0.8681 (m-70) cc_final: 0.8207 (m-70) REVERT: R 340 LEU cc_start: 0.8888 (mt) cc_final: 0.7271 (pp) outliers start: 41 outliers final: 36 residues processed: 246 average time/residue: 0.0890 time to fit residues: 30.6250 Evaluate side-chains 262 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 99 CYS Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 36 TRP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 253 ILE Chi-restraints excluded: chain R residue 309 CYS Chi-restraints excluded: chain R residue 311 ASN Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 317 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 41 optimal weight: 0.4980 chunk 11 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.230718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.188456 restraints weight = 12916.962| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 4.40 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8407 Z= 0.205 Angle : 0.760 13.387 11439 Z= 0.391 Chirality : 0.048 0.301 1318 Planarity : 0.006 0.070 1408 Dihedral : 6.836 59.485 1200 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.78 % Allowed : 22.15 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.27), residues: 997 helix: 0.15 (0.34), residues: 214 sheet: -0.25 (0.29), residues: 330 loop : -0.72 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 312 TYR 0.023 0.002 TYR L 93 PHE 0.043 0.002 PHE R 173 TRP 0.075 0.003 TRP L 36 HIS 0.016 0.002 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 8402) covalent geometry : angle 0.75785 (11429) SS BOND : bond 0.00438 ( 5) SS BOND : angle 2.10197 ( 10) hydrogen bonds : bond 0.04020 ( 353) hydrogen bonds : angle 5.96029 ( 1023) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2609.21 seconds wall clock time: 45 minutes 35.82 seconds (2735.82 seconds total)