Starting phenix.real_space_refine on Tue Apr 29 01:47:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e82_47700/04_2025/9e82_47700_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e82_47700/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9e82_47700/04_2025/9e82_47700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e82_47700/04_2025/9e82_47700.map" model { file = "/net/cci-nas-00/data/ceres_data/9e82_47700/04_2025/9e82_47700_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e82_47700/04_2025/9e82_47700_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.95, per 1000 atoms: 0.73 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: 2.40 Conformation dependent library (CDL) restraints added in 996.5 milliseconds 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: 1.10 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: 2.76 Time building geometry restraints manager: 2.79 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: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.920 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (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 TRP 0.008 0.001 TRP H 50 HIS 0.004 0.001 HIS A 353 PHE 0.009 0.001 PHE A 27 TYR 0.008 0.001 TYR L 94 ARG 0.002 0.000 ARG L 143 Details of bonding type rmsd hydrogen bonds : bond 0.14274 ( 353) hydrogen bonds : angle 6.85870 ( 1023) SS BOND : bond 0.00234 ( 5) SS BOND : angle 0.64746 ( 10) covalent geometry : bond 0.00316 ( 8402) covalent geometry : angle 0.52872 (11429) *********************** 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 : 0.816 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: 0.2081 time to fit residues: 87.7820 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 : 0.846 ------------------------------------------------------------------------------- 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 85 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 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** 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 = 0.4634 r_free = 0.4634 target = 0.228420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.179075 restraints weight = 12826.931| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 4.19 r_work: 0.3872 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8407 Z= 0.242 Angle : 0.709 8.870 11439 Z= 0.370 Chirality : 0.047 0.164 1318 Planarity : 0.006 0.082 1408 Dihedral : 6.921 54.624 1211 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.02 % Allowed : 12.92 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.28), residues: 997 helix: 0.94 (0.34), residues: 206 sheet: -0.90 (0.28), residues: 358 loop : -0.47 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 36 HIS 0.006 0.001 HIS H 38 PHE 0.025 0.002 PHE R 173 TYR 0.019 0.002 TYR L 141 ARG 0.007 0.001 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 353) hydrogen bonds : angle 6.03408 ( 1023) SS BOND : bond 0.00273 ( 5) SS BOND : angle 1.14860 ( 10) covalent geometry : bond 0.00538 ( 8402) covalent geometry : angle 0.70830 (11429) *********************** 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 303 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 0.838 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: A 7 ARG cc_start: 0.8608 (mtm110) cc_final: 0.8059 (ttp-110) REVERT: A 9 PHE cc_start: 0.8742 (m-80) cc_final: 0.8377 (m-80) REVERT: A 44 ASP cc_start: 0.5473 (p0) cc_final: 0.5123 (p0) REVERT: A 58 THR cc_start: 0.8235 (m) cc_final: 0.7818 (p) REVERT: A 87 PHE cc_start: 0.8393 (t80) cc_final: 0.8048 (t80) REVERT: A 122 ASN cc_start: 0.7822 (t0) cc_final: 0.7205 (t0) REVERT: H 53 SER cc_start: 0.8320 (t) cc_final: 0.7918 (p) REVERT: H 90 ARG cc_start: 0.7542 (mpp80) cc_final: 0.7299 (mpt-90) REVERT: H 102 LYS cc_start: 0.7558 (tptt) cc_final: 0.7141 (tptm) REVERT: H 139 SER cc_start: 0.5702 (t) cc_final: 0.4958 (p) REVERT: H 162 LYS cc_start: 0.7538 (tttp) cc_final: 0.6776 (tttp) REVERT: H 190 GLN cc_start: 0.7933 (tp-100) cc_final: 0.7687 (tp40) REVERT: H 228 LYS cc_start: 0.8259 (tptm) cc_final: 0.7849 (mttt) REVERT: L 28 GLN cc_start: 0.7718 (mp10) cc_final: 0.7434 (mm110) REVERT: L 48 LEU cc_start: 0.7606 (mt) cc_final: 0.7376 (mm) REVERT: L 56 TYR cc_start: 0.7370 (t80) cc_final: 0.6982 (t80) REVERT: L 71 ASP cc_start: 0.8114 (t0) cc_final: 0.7900 (t0) REVERT: L 72 PHE cc_start: 0.8908 (m-80) cc_final: 0.8698 (m-80) REVERT: L 86 THR cc_start: 0.7636 (OUTLIER) cc_final: 0.7212 (m) REVERT: L 105 VAL cc_start: 0.8263 (t) cc_final: 0.7691 (p) REVERT: L 164 VAL cc_start: 0.8482 (t) cc_final: 0.7294 (p) REVERT: R 277 PHE cc_start: 0.7164 (t80) cc_final: 0.6879 (t80) REVERT: R 298 HIS cc_start: 0.8668 (m-70) cc_final: 0.8242 (m-70) REVERT: R 340 LEU cc_start: 0.8857 (mt) cc_final: 0.7490 (pp) REVERT: R 342 LYS cc_start: 0.8408 (tmtt) cc_final: 0.8152 (tptp) outliers start: 37 outliers final: 24 residues processed: 286 average time/residue: 0.2010 time to fit residues: 77.1894 Evaluate side-chains 277 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 252 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 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 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 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 136 THR 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 24 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 29 optimal weight: 0.0010 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 81 optimal weight: 0.0970 chunk 93 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 87 optimal weight: 0.0670 overall best weight: 0.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 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 = 0.4707 r_free = 0.4707 target = 0.235896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.188323 restraints weight = 13001.492| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 4.20 r_work: 0.4002 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8407 Z= 0.132 Angle : 0.668 9.348 11439 Z= 0.341 Chirality : 0.045 0.161 1318 Planarity : 0.006 0.083 1408 Dihedral : 6.647 59.332 1201 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.93 % Allowed : 16.94 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.28), residues: 997 helix: 1.12 (0.35), residues: 203 sheet: -0.52 (0.28), residues: 354 loop : -0.45 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 36 HIS 0.026 0.002 HIS R 121 PHE 0.034 0.002 PHE R 173 TYR 0.030 0.001 TYR L 141 ARG 0.004 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 353) hydrogen bonds : angle 5.68299 ( 1023) SS BOND : bond 0.00901 ( 5) SS BOND : angle 1.84004 ( 10) covalent geometry : bond 0.00287 ( 8402) covalent geometry : angle 0.66603 (11429) *********************** 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 280 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 0.882 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: 0.8477 (m-80) cc_final: 0.8175 (m-80) REVERT: A 19 THR cc_start: 0.5504 (OUTLIER) cc_final: 0.4991 (p) REVERT: A 58 THR cc_start: 0.8009 (m) cc_final: 0.7674 (p) REVERT: A 104 LEU cc_start: -0.0527 (OUTLIER) cc_final: -0.1255 (mt) REVERT: A 169 ARG cc_start: 0.7663 (mtm180) cc_final: 0.6702 (mtm180) REVERT: H 5 VAL cc_start: 0.8125 (t) cc_final: 0.7192 (t) REVERT: H 6 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7213 (tm-30) REVERT: H 102 LYS cc_start: 0.7166 (tptt) cc_final: 0.6757 (tptm) REVERT: H 112 LEU cc_start: 0.7885 (mt) cc_final: 0.7524 (mt) REVERT: H 129 THR cc_start: 0.8309 (m) cc_final: 0.8059 (p) REVERT: H 190 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7752 (tp40) REVERT: H 228 LYS cc_start: 0.8167 (tptm) cc_final: 0.7849 (tttt) REVERT: L 28 GLN cc_start: 0.7791 (mp10) cc_final: 0.7586 (mm110) REVERT: L 50 TYR cc_start: 0.8420 (p90) cc_final: 0.7866 (p90) REVERT: L 56 TYR cc_start: 0.7280 (t80) cc_final: 0.7001 (t80) REVERT: L 71 ASP cc_start: 0.8101 (t0) cc_final: 0.7795 (t0) REVERT: L 72 PHE cc_start: 0.8862 (m-80) cc_final: 0.8651 (m-80) REVERT: L 105 VAL cc_start: 0.8256 (t) cc_final: 0.7588 (p) REVERT: L 193 TYR cc_start: 0.4824 (m-80) cc_final: 0.4581 (m-80) REVERT: R 277 PHE cc_start: 0.7047 (t80) cc_final: 0.6732 (t80) REVERT: R 298 HIS cc_start: 0.8694 (m-70) cc_final: 0.8235 (m-70) outliers start: 27 outliers final: 20 residues processed: 272 average time/residue: 0.2014 time to fit residues: 73.6135 Evaluate side-chains 259 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 116 TYR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 59 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.0170 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.0370 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN R 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.235202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.186988 restraints weight = 12857.381| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 4.19 r_work: 0.3939 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8407 Z= 0.160 Angle : 0.706 14.527 11439 Z= 0.353 Chirality : 0.047 0.258 1318 Planarity : 0.006 0.083 1408 Dihedral : 6.689 58.807 1201 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.89 % Allowed : 17.05 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.27), residues: 997 helix: 0.89 (0.34), residues: 207 sheet: -0.37 (0.29), residues: 348 loop : -0.54 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 39 HIS 0.017 0.002 HIS R 121 PHE 0.040 0.002 PHE R 173 TYR 0.027 0.001 TYR L 141 ARG 0.011 0.001 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 353) hydrogen bonds : angle 5.68402 ( 1023) SS BOND : bond 0.00603 ( 5) SS BOND : angle 1.50570 ( 10) covalent geometry : bond 0.00354 ( 8402) covalent geometry : angle 0.70526 (11429) *********************** 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 293 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 0.885 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: 0.8521 (m-80) cc_final: 0.8220 (m-80) REVERT: A 19 THR cc_start: 0.5589 (OUTLIER) cc_final: 0.5095 (p) REVERT: A 58 THR cc_start: 0.8137 (m) cc_final: 0.7786 (p) REVERT: A 104 LEU cc_start: -0.0927 (OUTLIER) cc_final: -0.1625 (mt) REVERT: A 169 ARG cc_start: 0.7690 (mtm180) cc_final: 0.7042 (mtm180) REVERT: A 293 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.5787 (mt) REVERT: H 6 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7226 (tm-30) REVERT: H 102 LYS cc_start: 0.7200 (tptt) cc_final: 0.6776 (tptm) REVERT: H 112 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7588 (mt) REVERT: H 129 THR cc_start: 0.8252 (m) cc_final: 0.8035 (p) REVERT: H 190 GLN cc_start: 0.8034 (tp-100) cc_final: 0.7721 (tp40) REVERT: H 228 LYS cc_start: 0.8203 (tptm) cc_final: 0.7819 (tttt) REVERT: L 28 GLN cc_start: 0.7888 (mp10) cc_final: 0.7605 (mm110) REVERT: L 50 TYR cc_start: 0.8417 (p90) cc_final: 0.7898 (p90) REVERT: L 56 TYR cc_start: 0.7179 (t80) cc_final: 0.6855 (t80) REVERT: L 71 ASP cc_start: 0.8182 (t0) cc_final: 0.7851 (t0) REVERT: L 94 TYR cc_start: 0.7543 (m-10) cc_final: 0.7223 (m-80) REVERT: L 105 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7461 (m) REVERT: L 164 VAL cc_start: 0.8182 (t) cc_final: 0.7930 (t) REVERT: R 277 PHE cc_start: 0.6995 (t80) cc_final: 0.6648 (t80) REVERT: R 298 HIS cc_start: 0.8681 (m-70) cc_final: 0.8206 (m-70) REVERT: R 340 LEU cc_start: 0.8909 (mt) cc_final: 0.7326 (pp) outliers start: 45 outliers final: 30 residues processed: 272 average time/residue: 0.2001 time to fit residues: 73.8315 Evaluate side-chains 276 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 293 LEU 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 97 ILE Chi-restraints excluded: chain L residue 98 THR 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 143 TYR Chi-restraints excluded: chain R residue 170 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 38 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 88 optimal weight: 5.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** 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 = 0.4620 r_free = 0.4620 target = 0.226806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.180214 restraints weight = 12755.019| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 4.20 r_work: 0.3847 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 8407 Z= 0.316 Angle : 0.773 10.972 11439 Z= 0.399 Chirality : 0.049 0.214 1318 Planarity : 0.006 0.065 1408 Dihedral : 7.105 59.486 1201 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 6.51 % Allowed : 16.94 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.27), residues: 997 helix: 0.44 (0.34), residues: 207 sheet: -0.61 (0.28), residues: 346 loop : -0.70 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP L 36 HIS 0.021 0.002 HIS H 106 PHE 0.037 0.002 PHE R 173 TYR 0.017 0.002 TYR L 141 ARG 0.006 0.001 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 353) hydrogen bonds : angle 6.16355 ( 1023) SS BOND : bond 0.00245 ( 5) SS BOND : angle 2.06953 ( 10) covalent geometry : bond 0.00700 ( 8402) covalent geometry : angle 0.77045 (11429) *********************** 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 294 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 234 time to evaluate : 0.857 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: A 9 PHE cc_start: 0.8801 (m-80) cc_final: 0.8560 (m-80) REVERT: A 19 THR cc_start: 0.5563 (OUTLIER) cc_final: 0.5081 (p) REVERT: A 58 THR cc_start: 0.8299 (m) cc_final: 0.7874 (p) REVERT: A 104 LEU cc_start: -0.0776 (OUTLIER) cc_final: -0.1015 (tp) REVERT: A 267 THR cc_start: 0.2195 (OUTLIER) cc_final: 0.1891 (m) REVERT: A 292 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7672 (tttm) REVERT: A 295 HIS cc_start: 0.7849 (OUTLIER) cc_final: 0.7526 (m90) REVERT: H 90 ARG cc_start: 0.7698 (mpt-90) cc_final: 0.7493 (mpt-90) REVERT: H 102 LYS cc_start: 0.7626 (tptt) cc_final: 0.6990 (tptm) REVERT: H 129 THR cc_start: 0.8320 (m) cc_final: 0.8028 (p) REVERT: H 162 LYS cc_start: 0.7755 (tttp) cc_final: 0.7220 (tttp) REVERT: H 190 GLN cc_start: 0.8118 (tp-100) cc_final: 0.7892 (tp40) REVERT: H 228 LYS cc_start: 0.8377 (tptm) cc_final: 0.8017 (tttt) REVERT: L 28 GLN cc_start: 0.7913 (mp10) cc_final: 0.7672 (mm110) REVERT: L 56 TYR cc_start: 0.7289 (t80) cc_final: 0.6790 (t80) REVERT: L 71 ASP cc_start: 0.8211 (t0) cc_final: 0.7846 (t0) REVERT: L 105 VAL cc_start: 0.8174 (t) cc_final: 0.7465 (m) REVERT: R 277 PHE cc_start: 0.7249 (t80) cc_final: 0.6870 (t80) REVERT: R 298 HIS cc_start: 0.8690 (m-70) cc_final: 0.8235 (m-70) REVERT: R 340 LEU cc_start: 0.8853 (mt) cc_final: 0.7547 (pt) outliers start: 60 outliers final: 44 residues processed: 263 average time/residue: 0.1838 time to fit residues: 67.1088 Evaluate side-chains 279 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 86 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 145 GLU 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 267 THR Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 295 HIS 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 77 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 198 SER Chi-restraints excluded: chain H residue 200 VAL 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 98 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 199 HIS Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 TYR Chi-restraints excluded: chain R residue 170 LEU 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 258 VAL 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 55 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 311 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 = 0.4647 r_free = 0.4647 target = 0.230052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.184201 restraints weight = 12844.440| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 4.17 r_work: 0.3885 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8407 Z= 0.211 Angle : 0.719 12.106 11439 Z= 0.369 Chirality : 0.047 0.237 1318 Planarity : 0.006 0.065 1408 Dihedral : 7.036 58.750 1201 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 5.43 % Allowed : 20.09 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.27), residues: 997 helix: 0.52 (0.35), residues: 207 sheet: -0.53 (0.28), residues: 349 loop : -0.65 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP L 36 HIS 0.018 0.002 HIS H 106 PHE 0.041 0.002 PHE R 173 TYR 0.021 0.002 TYR L 93 ARG 0.007 0.000 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 353) hydrogen bonds : angle 5.95664 ( 1023) SS BOND : bond 0.00272 ( 5) SS BOND : angle 1.65113 ( 10) covalent geometry : bond 0.00476 ( 8402) covalent geometry : angle 0.71721 (11429) *********************** 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 280 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 230 time to evaluate : 0.854 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 9 PHE cc_start: 0.8749 (m-80) cc_final: 0.8536 (m-80) REVERT: A 19 THR cc_start: 0.5636 (OUTLIER) cc_final: 0.5136 (p) REVERT: A 58 THR cc_start: 0.8210 (m) cc_final: 0.7796 (p) REVERT: A 285 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7445 (mtm180) REVERT: A 292 LYS cc_start: 0.7769 (tttt) cc_final: 0.7386 (tttm) REVERT: H 6 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7216 (tm-30) REVERT: H 22 ARG cc_start: 0.8018 (tpt-90) cc_final: 0.7791 (tpt-90) REVERT: H 90 ARG cc_start: 0.7899 (mpt-90) cc_final: 0.7546 (mmt90) REVERT: H 102 LYS cc_start: 0.7457 (tptt) cc_final: 0.6907 (tptm) REVERT: H 129 THR cc_start: 0.8317 (m) cc_final: 0.8049 (p) REVERT: H 141 PHE cc_start: 0.7359 (m-80) cc_final: 0.6963 (m-10) REVERT: H 190 GLN cc_start: 0.8150 (tp-100) cc_final: 0.7860 (tm-30) REVERT: H 228 LYS cc_start: 0.8357 (tptm) cc_final: 0.7937 (mttt) REVERT: L 28 GLN cc_start: 0.7938 (mp10) cc_final: 0.7657 (mm110) REVERT: L 50 TYR cc_start: 0.8544 (p90) cc_final: 0.7930 (p90) REVERT: L 56 TYR cc_start: 0.7226 (t80) cc_final: 0.6878 (t80) REVERT: L 71 ASP cc_start: 0.8191 (t0) cc_final: 0.7801 (t0) REVERT: L 143 ARG cc_start: 0.8901 (mmm-85) cc_final: 0.8469 (tpp80) REVERT: R 277 PHE cc_start: 0.7291 (t80) cc_final: 0.6905 (t80) REVERT: R 298 HIS cc_start: 0.8664 (m-70) cc_final: 0.8208 (m-70) REVERT: R 340 LEU cc_start: 0.8869 (mt) cc_final: 0.7508 (pp) outliers start: 50 outliers final: 39 residues processed: 253 average time/residue: 0.1866 time to fit residues: 65.3029 Evaluate side-chains 269 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 86 SER 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 285 ARG 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 184 THR Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain L residue 48 LEU 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 L residue 199 HIS Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 55 PHE 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 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 311 ASN Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 317 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 GLN ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 311 ASN R 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.233722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.184700 restraints weight = 12900.395| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 4.22 r_work: 0.3914 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4179 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= 0.171 Angle : 0.706 11.440 11439 Z= 0.363 Chirality : 0.047 0.241 1318 Planarity : 0.006 0.070 1408 Dihedral : 6.845 57.874 1201 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.78 % Allowed : 21.82 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.27), residues: 997 helix: 0.57 (0.34), residues: 213 sheet: -0.47 (0.28), residues: 347 loop : -0.66 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP L 36 HIS 0.009 0.001 HIS H 106 PHE 0.027 0.002 PHE L 140 TYR 0.023 0.002 TYR L 93 ARG 0.006 0.000 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 353) hydrogen bonds : angle 5.83321 ( 1023) SS BOND : bond 0.00313 ( 5) SS BOND : angle 1.59813 ( 10) covalent geometry : bond 0.00395 ( 8402) covalent geometry : angle 0.70480 (11429) *********************** 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 276 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.960 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 19 THR cc_start: 0.5586 (OUTLIER) cc_final: 0.5091 (p) REVERT: A 58 THR cc_start: 0.8171 (m) cc_final: 0.7742 (p) REVERT: A 104 LEU cc_start: -0.0780 (OUTLIER) cc_final: -0.1580 (mt) REVERT: A 285 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7645 (mtm180) REVERT: H 6 GLN cc_start: 0.7370 (tm-30) cc_final: 0.7126 (tm-30) REVERT: H 90 ARG cc_start: 0.7886 (mpt-90) cc_final: 0.7616 (mmt90) REVERT: H 102 LYS cc_start: 0.7336 (tptt) cc_final: 0.7004 (tptm) REVERT: H 129 THR cc_start: 0.8239 (m) cc_final: 0.7986 (p) REVERT: H 141 PHE cc_start: 0.7337 (m-80) cc_final: 0.6990 (m-10) REVERT: H 190 GLN cc_start: 0.8022 (tp-100) cc_final: 0.7799 (tp40) REVERT: H 228 LYS cc_start: 0.8344 (tptm) cc_final: 0.7940 (tttt) REVERT: L 28 GLN cc_start: 0.7965 (mp10) cc_final: 0.7696 (mm110) REVERT: L 50 TYR cc_start: 0.8535 (p90) cc_final: 0.7976 (p90) REVERT: L 56 TYR cc_start: 0.7174 (t80) cc_final: 0.6728 (t80) REVERT: L 71 ASP cc_start: 0.8152 (t0) cc_final: 0.7723 (t0) REVERT: L 143 ARG cc_start: 0.8889 (mmm-85) cc_final: 0.8510 (tpp80) REVERT: R 277 PHE cc_start: 0.7304 (t80) cc_final: 0.6916 (t80) REVERT: R 298 HIS cc_start: 0.8701 (m-70) cc_final: 0.8222 (m-70) REVERT: R 340 LEU cc_start: 0.8959 (mt) cc_final: 0.7578 (pp) outliers start: 44 outliers final: 36 residues processed: 254 average time/residue: 0.2315 time to fit residues: 81.1444 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 : 1.517 ------------------------------------------------------------------------------- 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 285 ARG 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 116 TYR 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 98 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 199 HIS Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 136 THR 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 253 ILE 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 75 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 28 optimal weight: 0.0000 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 64 optimal weight: 0.0870 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4663 r_free = 0.4663 target = 0.231745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.182144 restraints weight = 13049.930| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 4.21 r_work: 0.3929 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8407 Z= 0.179 Angle : 0.720 10.343 11439 Z= 0.368 Chirality : 0.047 0.281 1318 Planarity : 0.006 0.099 1408 Dihedral : 6.707 58.719 1200 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.32 % Allowed : 21.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.27), residues: 997 helix: 0.46 (0.33), residues: 213 sheet: -0.38 (0.29), residues: 347 loop : -0.64 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP L 36 HIS 0.011 0.001 HIS H 106 PHE 0.027 0.002 PHE L 140 TYR 0.023 0.002 TYR L 93 ARG 0.008 0.000 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 353) hydrogen bonds : angle 5.76842 ( 1023) SS BOND : bond 0.00258 ( 5) SS BOND : angle 1.82910 ( 10) covalent geometry : bond 0.00409 ( 8402) covalent geometry : angle 0.71787 (11429) *********************** 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 276 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 227 time to evaluate : 0.841 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 19 THR cc_start: 0.5529 (OUTLIER) cc_final: 0.5045 (p) REVERT: A 58 THR cc_start: 0.8168 (m) cc_final: 0.7720 (p) REVERT: A 104 LEU cc_start: -0.0916 (OUTLIER) cc_final: -0.1710 (mt) REVERT: A 285 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7200 (mtm-85) REVERT: A 289 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6946 (mt) REVERT: H 22 ARG cc_start: 0.8107 (tpt-90) cc_final: 0.7783 (tpt90) REVERT: H 102 LYS cc_start: 0.7379 (tptt) cc_final: 0.7007 (tptm) REVERT: H 129 THR cc_start: 0.8242 (m) cc_final: 0.7955 (p) REVERT: H 141 PHE cc_start: 0.7452 (m-80) cc_final: 0.7156 (m-80) REVERT: H 190 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7834 (tp40) REVERT: H 195 TYR cc_start: 0.8583 (m-10) cc_final: 0.8367 (m-10) REVERT: H 228 LYS cc_start: 0.8328 (tptm) cc_final: 0.7897 (tttt) REVERT: L 28 GLN cc_start: 0.7917 (mp10) cc_final: 0.7638 (mm110) REVERT: L 38 GLN cc_start: 0.7915 (tt0) cc_final: 0.7417 (tm-30) REVERT: L 50 TYR cc_start: 0.8482 (p90) cc_final: 0.7910 (p90) REVERT: L 56 TYR cc_start: 0.7135 (t80) cc_final: 0.6696 (t80) REVERT: L 71 ASP cc_start: 0.8133 (t0) cc_final: 0.7704 (t0) REVERT: L 143 ARG cc_start: 0.8894 (mmm-85) cc_final: 0.8496 (tpp80) REVERT: R 277 PHE cc_start: 0.7349 (t80) cc_final: 0.6944 (t80) REVERT: R 298 HIS cc_start: 0.8742 (m-70) cc_final: 0.8253 (m-70) REVERT: R 340 LEU cc_start: 0.8949 (mt) cc_final: 0.7597 (pp) outliers start: 49 outliers final: 41 residues processed: 251 average time/residue: 0.1812 time to fit residues: 62.9858 Evaluate side-chains 263 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 218 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 285 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 314 ILE 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 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 59 VAL 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 L residue 118 ILE Chi-restraints excluded: chain L residue 199 HIS Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 136 THR 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 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 6 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.231050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.181274 restraints weight = 12947.199| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 4.20 r_work: 0.3921 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8407 Z= 0.202 Angle : 0.742 11.824 11439 Z= 0.382 Chirality : 0.047 0.283 1318 Planarity : 0.006 0.091 1408 Dihedral : 6.779 59.241 1200 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 5.32 % Allowed : 22.15 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.27), residues: 997 helix: 0.36 (0.34), residues: 213 sheet: -0.35 (0.29), residues: 342 loop : -0.72 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP L 36 HIS 0.009 0.001 HIS H 106 PHE 0.029 0.002 PHE L 140 TYR 0.022 0.002 TYR L 93 ARG 0.007 0.000 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 353) hydrogen bonds : angle 5.87169 ( 1023) SS BOND : bond 0.00246 ( 5) SS BOND : angle 1.79883 ( 10) covalent geometry : bond 0.00463 ( 8402) covalent geometry : angle 0.74048 (11429) *********************** 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 274 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 225 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.5572 (OUTLIER) cc_final: 0.4925 (t) REVERT: A 58 THR cc_start: 0.8178 (m) cc_final: 0.7725 (p) REVERT: A 104 LEU cc_start: -0.0741 (OUTLIER) cc_final: -0.1607 (mt) REVERT: A 285 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7257 (mtm-85) REVERT: A 289 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7180 (mt) REVERT: A 292 LYS cc_start: 0.7409 (tmtt) cc_final: 0.6240 (tmtt) REVERT: H 6 GLN cc_start: 0.7457 (tm-30) cc_final: 0.7249 (tm-30) REVERT: H 22 ARG cc_start: 0.8041 (tpt-90) cc_final: 0.7823 (tpt-90) REVERT: H 90 ARG cc_start: 0.7918 (mpt-90) cc_final: 0.7691 (mmt90) REVERT: H 102 LYS cc_start: 0.7408 (tptt) cc_final: 0.7018 (tptm) REVERT: H 129 THR cc_start: 0.8248 (m) cc_final: 0.7970 (p) REVERT: H 141 PHE cc_start: 0.7566 (m-80) cc_final: 0.7251 (m-80) REVERT: H 228 LYS cc_start: 0.8383 (tptm) cc_final: 0.7986 (tttt) REVERT: L 28 GLN cc_start: 0.7909 (mp10) cc_final: 0.7636 (mm110) REVERT: L 38 GLN cc_start: 0.7936 (tt0) cc_final: 0.7477 (tm-30) REVERT: L 50 TYR cc_start: 0.8547 (p90) cc_final: 0.7979 (p90) REVERT: L 56 TYR cc_start: 0.7099 (t80) cc_final: 0.6744 (t80) REVERT: L 71 ASP cc_start: 0.8055 (t0) cc_final: 0.7537 (t0) REVERT: L 143 ARG cc_start: 0.8886 (mmm-85) cc_final: 0.8583 (tpp80) REVERT: R 277 PHE cc_start: 0.7437 (t80) cc_final: 0.7059 (t80) REVERT: R 298 HIS cc_start: 0.8696 (m-70) cc_final: 0.8232 (m-70) outliers start: 49 outliers final: 42 residues processed: 249 average time/residue: 0.1887 time to fit residues: 64.9762 Evaluate side-chains 266 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 285 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 314 ILE 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 104 MET Chi-restraints excluded: chain H residue 106 HIS 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 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 59 VAL 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 L residue 118 ILE Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 136 THR 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 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 Chi-restraints excluded: chain R residue 337 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 9 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 29 optimal weight: 0.0870 chunk 20 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.235415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.186179 restraints weight = 12908.620| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 4.22 r_work: 0.3943 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8407 Z= 0.166 Angle : 0.765 11.781 11439 Z= 0.391 Chirality : 0.048 0.306 1318 Planarity : 0.006 0.086 1408 Dihedral : 6.771 59.804 1200 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.78 % Allowed : 23.13 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.27), residues: 997 helix: 0.42 (0.34), residues: 212 sheet: -0.29 (0.29), residues: 342 loop : -0.76 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP L 36 HIS 0.006 0.001 HIS R 121 PHE 0.030 0.002 PHE L 140 TYR 0.022 0.002 TYR L 93 ARG 0.007 0.000 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 353) hydrogen bonds : angle 5.81779 ( 1023) SS BOND : bond 0.00347 ( 5) SS BOND : angle 2.02609 ( 10) covalent geometry : bond 0.00383 ( 8402) covalent geometry : angle 0.76273 (11429) ********************** 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 263 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.5669 (OUTLIER) cc_final: 0.5067 (t) REVERT: A 58 THR cc_start: 0.7998 (m) cc_final: 0.7552 (p) REVERT: A 104 LEU cc_start: -0.0837 (OUTLIER) cc_final: -0.1709 (mt) REVERT: A 285 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7143 (mtm-85) REVERT: A 289 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7065 (mt) REVERT: A 292 LYS cc_start: 0.7315 (tmtt) cc_final: 0.6081 (tmtt) REVERT: H 6 GLN cc_start: 0.7394 (tm-30) cc_final: 0.7163 (tm-30) REVERT: H 90 ARG cc_start: 0.7941 (mpt-90) cc_final: 0.7728 (mmt90) REVERT: H 102 LYS cc_start: 0.7327 (tptt) cc_final: 0.6972 (tptm) REVERT: H 129 THR cc_start: 0.8251 (m) cc_final: 0.8002 (p) REVERT: H 141 PHE cc_start: 0.7508 (m-80) cc_final: 0.7262 (m-80) REVERT: H 228 LYS cc_start: 0.8391 (tptm) cc_final: 0.7957 (tttt) REVERT: L 28 GLN cc_start: 0.7916 (mp10) cc_final: 0.7645 (mm110) REVERT: L 38 GLN cc_start: 0.8000 (tt0) cc_final: 0.7544 (tm-30) REVERT: L 50 TYR cc_start: 0.8461 (p90) cc_final: 0.7909 (p90) REVERT: L 56 TYR cc_start: 0.7020 (t80) cc_final: 0.6660 (t80) REVERT: L 71 ASP cc_start: 0.8095 (t0) cc_final: 0.7563 (t0) REVERT: L 143 ARG cc_start: 0.8931 (mmm-85) cc_final: 0.8424 (tpp80) REVERT: R 44 LEU cc_start: 0.9084 (mt) cc_final: 0.8753 (pp) REVERT: R 213 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8237 (mm-30) REVERT: R 277 PHE cc_start: 0.7444 (t80) cc_final: 0.7064 (t80) REVERT: R 298 HIS cc_start: 0.8678 (m-70) cc_final: 0.8174 (m-70) outliers start: 44 outliers final: 35 residues processed: 246 average time/residue: 0.1855 time to fit residues: 62.8304 Evaluate side-chains 252 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 285 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 314 ILE 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 104 MET 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 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 98 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 118 ILE Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 136 THR 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 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 69 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 55 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 44 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 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 = 0.4717 r_free = 0.4717 target = 0.237038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.187626 restraints weight = 13090.402| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 4.32 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8407 Z= 0.158 Angle : 0.756 11.485 11439 Z= 0.391 Chirality : 0.047 0.314 1318 Planarity : 0.006 0.096 1408 Dihedral : 6.641 58.480 1200 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.34 % Allowed : 24.21 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.27), residues: 997 helix: 0.47 (0.34), residues: 212 sheet: -0.22 (0.29), residues: 340 loop : -0.70 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP L 36 HIS 0.006 0.001 HIS R 121 PHE 0.028 0.002 PHE L 140 TYR 0.022 0.001 TYR L 93 ARG 0.007 0.000 ARG A 236 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 353) hydrogen bonds : angle 5.70872 ( 1023) SS BOND : bond 0.01118 ( 5) SS BOND : angle 1.61790 ( 10) covalent geometry : bond 0.00365 ( 8402) covalent geometry : angle 0.75502 (11429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5128.83 seconds wall clock time: 89 minutes 21.26 seconds (5361.26 seconds total)