Starting phenix.real_space_refine on Fri Jun 6 19:59:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f76_28896/06_2025/8f76_28896.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f76_28896/06_2025/8f76_28896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f76_28896/06_2025/8f76_28896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f76_28896/06_2025/8f76_28896.map" model { file = "/net/cci-nas-00/data/ceres_data/8f76_28896/06_2025/8f76_28896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f76_28896/06_2025/8f76_28896.cif" } resolution = 3.1 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= 0.015 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5195 2.51 5 N 1428 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8170 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2363 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "X" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1818 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain breaks: 4 Chain: "Y" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Z" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PPI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.62, per 1000 atoms: 0.69 Number of scatterers: 8170 At special positions: 0 Unit cell: (82.62, 98.82, 136.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1490 8.00 N 1428 7.00 C 5195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 178 " 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: 2.02 Conformation dependent library (CDL) restraints added in 1.2 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 43.1% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 22 through 48 Proline residue: A 29 - end of helix removed outlier: 3.932A pdb=" N SER A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.579A pdb=" N LEU A 54 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS A 55 " --> pdb=" O ARG A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 55' Processing helix chain 'A' and resid 56 through 87 Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 93 through 127 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 136 through 156 Processing helix chain 'A' and resid 156 through 163 removed outlier: 3.924A pdb=" N LYS A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.635A pdb=" N ALA A 187 " --> pdb=" O MET A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 225 Processing helix chain 'A' and resid 229 through 263 removed outlier: 3.529A pdb=" N ARG A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 268 through 281 removed outlier: 3.984A pdb=" N ARG A 272 " --> pdb=" O HIS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 Proline residue: A 288 - end of helix Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.710A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.980A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 15 through 40 Processing helix chain 'X' and resid 52 through 58 Processing helix chain 'X' and resid 233 through 240 removed outlier: 4.065A pdb=" N ASN X 239 " --> pdb=" O GLN X 236 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP X 240 " --> pdb=" O CYS X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 279 Processing helix chain 'X' and resid 280 through 283 removed outlier: 3.828A pdb=" N ARG X 283 " --> pdb=" O ARG X 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 280 through 283' Processing helix chain 'X' and resid 293 through 303 Processing helix chain 'X' and resid 307 through 312 removed outlier: 4.142A pdb=" N TYR X 311 " --> pdb=" O LYS X 307 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 318 removed outlier: 3.520A pdb=" N TYR X 318 " --> pdb=" O PHE X 315 " (cutoff:3.500A) Processing helix chain 'X' and resid 331 through 351 removed outlier: 4.178A pdb=" N THR X 335 " --> pdb=" O ASP X 331 " (cutoff:3.500A) Processing helix chain 'X' and resid 370 through 391 Processing helix chain 'Y' and resid 4 through 26 Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Z' and resid 8 through 24 removed outlier: 3.907A pdb=" N ASN Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 45 Processing helix chain 'Z' and resid 46 through 48 No H-bonds generated for 'chain 'Z' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.726A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 207 through 214 removed outlier: 4.334A pdb=" N VAL X 224 " --> pdb=" O LEU X 45 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG X 42 " --> pdb=" O ALA X 243 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE X 245 " --> pdb=" O ARG X 42 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU X 44 " --> pdb=" O ILE X 245 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL X 247 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU X 46 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ASP X 249 " --> pdb=" O LEU X 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 46 through 52 removed outlier: 5.486A pdb=" N THR Y 47 " --> pdb=" O ASN Y 340 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN Y 340 " --> pdb=" O THR Y 47 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE Y 335 " --> pdb=" O SER Y 331 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER Y 331 " --> pdb=" O PHE Y 335 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS Y 337 " --> pdb=" O THR Y 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Y' and resid 58 through 63 removed outlier: 3.710A pdb=" N ALA Y 60 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU Y 70 " --> pdb=" O TRP Y 82 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASP Y 83 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LYS Y 89 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 100 through 105 removed outlier: 6.631A pdb=" N GLY Y 115 " --> pdb=" O MET Y 101 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N CYS Y 103 " --> pdb=" O ALA Y 113 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA Y 113 " --> pdb=" O CYS Y 103 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR Y 105 " --> pdb=" O TYR Y 111 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TYR Y 111 " --> pdb=" O TYR Y 105 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY Y 116 " --> pdb=" O ILE Y 120 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE Y 120 " --> pdb=" O GLY Y 116 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN Y 125 " --> pdb=" O VAL Y 135 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL Y 135 " --> pdb=" O ASN Y 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Y' and resid 146 through 151 removed outlier: 4.177A pdb=" N THR Y 165 " --> pdb=" O SER Y 161 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASP Y 170 " --> pdb=" O GLN Y 176 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN Y 176 " --> pdb=" O ASP Y 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 187 through 192 removed outlier: 4.564A pdb=" N SER Y 207 " --> pdb=" O ALA Y 203 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP Y 212 " --> pdb=" O CYS Y 218 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS Y 218 " --> pdb=" O ASP Y 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 229 through 234 removed outlier: 6.189A pdb=" N ASP Y 254 " --> pdb=" O GLU Y 260 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU Y 260 " --> pdb=" O ASP Y 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Y' and resid 273 through 278 removed outlier: 3.835A pdb=" N SER Y 275 " --> pdb=" O GLY Y 288 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP Y 298 " --> pdb=" O ARG Y 304 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG Y 304 " --> pdb=" O ASP Y 298 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1278 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: 2.55 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2320 1.34 - 1.45: 1421 1.45 - 1.57: 4512 1.57 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 8336 Sorted by residual: bond pdb=" CG1 ILE X 285 " pdb=" CD1 ILE X 285 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.00e+00 bond pdb=" CB PHE A 101 " pdb=" CG PHE A 101 " ideal model delta sigma weight residual 1.502 1.540 -0.038 2.30e-02 1.89e+03 2.76e+00 bond pdb=" C2 PPI A 401 " pdb=" C3 PPI A 401 " ideal model delta sigma weight residual 1.519 1.487 0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" CB THR Y 274 " pdb=" CG2 THR Y 274 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" CA THR Y 87 " pdb=" C THR Y 87 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.34e-02 5.57e+03 1.83e+00 ... (remaining 8331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 10927 2.10 - 4.21: 292 4.21 - 6.31: 46 6.31 - 8.42: 17 8.42 - 10.52: 5 Bond angle restraints: 11287 Sorted by residual: angle pdb=" C THR Y 86 " pdb=" N THR Y 87 " pdb=" CA THR Y 87 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" CA PRO A 283 " pdb=" C PRO A 283 " pdb=" N PRO A 284 " ideal model delta sigma weight residual 117.93 122.25 -4.32 1.20e+00 6.94e-01 1.29e+01 angle pdb=" C TYR A 188 " pdb=" N ALA A 189 " pdb=" CA ALA A 189 " ideal model delta sigma weight residual 121.54 128.36 -6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" N PRO A 283 " pdb=" CA PRO A 283 " pdb=" C PRO A 283 " ideal model delta sigma weight residual 110.70 114.92 -4.22 1.22e+00 6.72e-01 1.20e+01 angle pdb=" CB MET A 77 " pdb=" CG MET A 77 " pdb=" SD MET A 77 " ideal model delta sigma weight residual 112.70 123.02 -10.32 3.00e+00 1.11e-01 1.18e+01 ... (remaining 11282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4450 17.96 - 35.92: 428 35.92 - 53.88: 78 53.88 - 71.84: 10 71.84 - 89.80: 10 Dihedral angle restraints: 4976 sinusoidal: 1957 harmonic: 3019 Sorted by residual: dihedral pdb=" CB CYS A 4 " pdb=" SG CYS A 4 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual -86.00 -136.74 50.74 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CA ASN A 41 " pdb=" C ASN A 41 " pdb=" N CYS A 42 " pdb=" CA CYS A 42 " ideal model delta harmonic sigma weight residual -180.00 -154.37 -25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ALA Y 60 " pdb=" C ALA Y 60 " pdb=" N MET Y 61 " pdb=" CA MET Y 61 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 4973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 906 0.050 - 0.100: 281 0.100 - 0.150: 80 0.150 - 0.200: 14 0.200 - 0.250: 4 Chirality restraints: 1285 Sorted by residual: chirality pdb=" CB VAL X 57 " pdb=" CA VAL X 57 " pdb=" CG1 VAL X 57 " pdb=" CG2 VAL X 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA TYR Y 59 " pdb=" N TYR Y 59 " pdb=" C TYR Y 59 " pdb=" CB TYR Y 59 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CG LEU Y 286 " pdb=" CB LEU Y 286 " pdb=" CD1 LEU Y 286 " pdb=" CD2 LEU Y 286 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1282 not shown) Planarity restraints: 1436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 39 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C PHE A 39 " -0.075 2.00e-02 2.50e+03 pdb=" O PHE A 39 " 0.028 2.00e-02 2.50e+03 pdb=" N GLY A 40 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Y 59 " -0.035 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR Y 59 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR Y 59 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR Y 59 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR Y 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR Y 59 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR Y 59 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR Y 59 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 156 " 0.055 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO A 157 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " 0.046 5.00e-02 4.00e+02 ... (remaining 1433 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1595 2.78 - 3.31: 7488 3.31 - 3.84: 14416 3.84 - 4.37: 17192 4.37 - 4.90: 29723 Nonbonded interactions: 70414 Sorted by model distance: nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.245 3.040 nonbonded pdb=" O PRO N 100 " pdb=" OG SER Y 227 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR Y 274 " pdb=" O VAL Y 315 " model vdw 2.279 3.040 nonbonded pdb=" OG SER Y 147 " pdb=" O VAL Y 187 " model vdw 2.285 3.040 nonbonded pdb=" O ILE Y 58 " pdb=" OG SER Y 316 " model vdw 2.288 3.040 ... (remaining 70409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.330 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8338 Z= 0.218 Angle : 0.853 10.521 11291 Z= 0.451 Chirality : 0.055 0.250 1285 Planarity : 0.007 0.082 1436 Dihedral : 14.684 89.799 3014 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.24), residues: 1020 helix: -0.63 (0.23), residues: 384 sheet: -0.65 (0.33), residues: 220 loop : -0.81 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP Y 99 HIS 0.005 0.001 HIS X 357 PHE 0.036 0.002 PHE A 101 TYR 0.057 0.003 TYR Y 59 ARG 0.016 0.001 ARG Y 197 Details of bonding type rmsd hydrogen bonds : bond 0.13409 ( 444) hydrogen bonds : angle 7.28748 ( 1278) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.37152 ( 4) covalent geometry : bond 0.00483 ( 8336) covalent geometry : angle 0.85357 (11287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.189 Fit side-chains REVERT: X 27 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6699 (mp0) REVERT: X 292 ASN cc_start: 0.7635 (m110) cc_final: 0.7412 (m110) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2757 time to fit residues: 42.6103 Evaluate side-chains 101 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.0170 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 ASN ** X 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN Y 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107428 restraints weight = 9512.429| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.98 r_work: 0.3038 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8338 Z= 0.271 Angle : 0.640 8.488 11291 Z= 0.338 Chirality : 0.046 0.148 1285 Planarity : 0.005 0.063 1436 Dihedral : 5.247 77.860 1129 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.90 % Allowed : 7.89 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1020 helix: 0.65 (0.26), residues: 382 sheet: -0.77 (0.34), residues: 220 loop : -0.45 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP X 281 HIS 0.005 0.001 HIS A 127 PHE 0.020 0.002 PHE X 246 TYR 0.037 0.002 TYR Y 59 ARG 0.004 0.000 ARG Y 49 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 444) hydrogen bonds : angle 5.78337 ( 1278) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.54021 ( 4) covalent geometry : bond 0.00641 ( 8336) covalent geometry : angle 0.64019 (11287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 190 ASP cc_start: 0.7576 (t70) cc_final: 0.7161 (t0) REVERT: Y 219 ARG cc_start: 0.7944 (mmt180) cc_final: 0.7532 (tpp80) REVERT: Z 31 SER cc_start: 0.7615 (m) cc_final: 0.7378 (m) outliers start: 8 outliers final: 4 residues processed: 125 average time/residue: 0.2469 time to fit residues: 40.3880 Evaluate side-chains 111 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain Y residue 189 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 35 GLN X 292 ASN Y 32 GLN Y 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111489 restraints weight = 9579.342| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.99 r_work: 0.3096 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8338 Z= 0.141 Angle : 0.521 5.926 11291 Z= 0.276 Chirality : 0.042 0.143 1285 Planarity : 0.004 0.058 1436 Dihedral : 5.056 89.820 1129 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.69 % Allowed : 11.05 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1020 helix: 1.26 (0.26), residues: 386 sheet: -0.73 (0.34), residues: 214 loop : -0.40 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Y 211 HIS 0.004 0.001 HIS X 220 PHE 0.020 0.001 PHE A 155 TYR 0.018 0.001 TYR Y 59 ARG 0.003 0.000 ARG Y 197 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 444) hydrogen bonds : angle 5.43079 ( 1278) SS BOND : bond 0.00238 ( 2) SS BOND : angle 0.47530 ( 4) covalent geometry : bond 0.00320 ( 8336) covalent geometry : angle 0.52118 (11287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 190 ASP cc_start: 0.7536 (t70) cc_final: 0.7134 (t0) REVERT: N 80 TYR cc_start: 0.8211 (m-80) cc_final: 0.7925 (m-80) REVERT: X 220 HIS cc_start: 0.8637 (t-170) cc_final: 0.7757 (t-90) REVERT: Z 31 SER cc_start: 0.7602 (m) cc_final: 0.7383 (m) outliers start: 15 outliers final: 9 residues processed: 119 average time/residue: 0.2449 time to fit residues: 38.0657 Evaluate side-chains 112 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 292 ASN Chi-restraints excluded: chain Y residue 189 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 42 optimal weight: 0.0030 chunk 59 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 35 ASN X 292 ASN Y 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110317 restraints weight = 9451.386| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.98 r_work: 0.3134 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8338 Z= 0.140 Angle : 0.509 6.615 11291 Z= 0.269 Chirality : 0.042 0.162 1285 Planarity : 0.004 0.056 1436 Dihedral : 4.908 88.367 1129 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.48 % Allowed : 11.50 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.27), residues: 1020 helix: 1.51 (0.27), residues: 387 sheet: -0.78 (0.34), residues: 215 loop : -0.32 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Y 211 HIS 0.005 0.001 HIS X 220 PHE 0.017 0.001 PHE A 155 TYR 0.017 0.001 TYR A 197 ARG 0.006 0.000 ARG Y 219 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 444) hydrogen bonds : angle 5.30078 ( 1278) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.43398 ( 4) covalent geometry : bond 0.00320 ( 8336) covalent geometry : angle 0.50925 (11287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 145 ILE cc_start: 0.8015 (mm) cc_final: 0.7806 (mt) REVERT: A 190 ASP cc_start: 0.7532 (t70) cc_final: 0.7111 (t0) REVERT: Y 312 ASP cc_start: 0.7467 (p0) cc_final: 0.7248 (p0) REVERT: Z 31 SER cc_start: 0.7608 (m) cc_final: 0.7385 (m) outliers start: 22 outliers final: 17 residues processed: 123 average time/residue: 0.2296 time to fit residues: 37.4942 Evaluate side-chains 124 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 292 ASN Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Y residue 276 VAL Chi-restraints excluded: chain Z residue 28 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 7 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 35 ASN X 35 GLN X 292 ASN Y 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108566 restraints weight = 9570.467| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.98 r_work: 0.3099 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8338 Z= 0.134 Angle : 0.497 6.393 11291 Z= 0.263 Chirality : 0.042 0.169 1285 Planarity : 0.004 0.055 1436 Dihedral : 4.834 88.726 1129 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.04 % Allowed : 12.63 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 1020 helix: 1.65 (0.27), residues: 388 sheet: -0.70 (0.34), residues: 212 loop : -0.34 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 211 HIS 0.003 0.001 HIS X 357 PHE 0.016 0.001 PHE A 155 TYR 0.016 0.001 TYR A 197 ARG 0.005 0.000 ARG Y 219 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 444) hydrogen bonds : angle 5.22328 ( 1278) SS BOND : bond 0.00237 ( 2) SS BOND : angle 0.40979 ( 4) covalent geometry : bond 0.00306 ( 8336) covalent geometry : angle 0.49742 (11287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 145 ILE cc_start: 0.7903 (mm) cc_final: 0.7699 (mt) REVERT: A 190 ASP cc_start: 0.7519 (t70) cc_final: 0.7071 (t0) REVERT: A 275 MET cc_start: 0.8326 (ttm) cc_final: 0.8052 (ttm) REVERT: Y 43 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7831 (mt) REVERT: Y 59 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8117 (m-80) REVERT: Z 31 SER cc_start: 0.7502 (m) cc_final: 0.7277 (m) outliers start: 27 outliers final: 19 residues processed: 131 average time/residue: 0.2328 time to fit residues: 40.3067 Evaluate side-chains 131 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 292 ASN Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Y residue 228 ASP Chi-restraints excluded: chain Y residue 276 VAL Chi-restraints excluded: chain Z residue 28 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN X 292 ASN Y 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104791 restraints weight = 9590.562| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.01 r_work: 0.3001 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8338 Z= 0.220 Angle : 0.557 7.445 11291 Z= 0.293 Chirality : 0.044 0.157 1285 Planarity : 0.004 0.053 1436 Dihedral : 4.990 88.374 1129 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.27 % Allowed : 13.64 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.27), residues: 1020 helix: 1.53 (0.27), residues: 386 sheet: -0.96 (0.33), residues: 227 loop : -0.25 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Y 211 HIS 0.004 0.001 HIS X 357 PHE 0.014 0.002 PHE A 155 TYR 0.018 0.002 TYR A 197 ARG 0.004 0.000 ARG Y 219 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 444) hydrogen bonds : angle 5.41370 ( 1278) SS BOND : bond 0.00319 ( 2) SS BOND : angle 0.48448 ( 4) covalent geometry : bond 0.00526 ( 8336) covalent geometry : angle 0.55704 (11287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.7855 (mmm) cc_final: 0.7360 (tpp) REVERT: A 145 ILE cc_start: 0.7810 (mm) cc_final: 0.7602 (mt) REVERT: A 190 ASP cc_start: 0.7552 (t70) cc_final: 0.7041 (t0) REVERT: Y 25 CYS cc_start: 0.7070 (t) cc_final: 0.6806 (t) REVERT: Y 43 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7789 (mp) REVERT: Y 59 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: Y 138 GLU cc_start: 0.8234 (tp30) cc_final: 0.7998 (tp30) REVERT: Z 31 SER cc_start: 0.7402 (m) cc_final: 0.7197 (m) outliers start: 29 outliers final: 23 residues processed: 133 average time/residue: 0.2359 time to fit residues: 41.5889 Evaluate side-chains 137 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 292 ASN Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Y residue 228 ASP Chi-restraints excluded: chain Y residue 275 SER Chi-restraints excluded: chain Y residue 276 VAL Chi-restraints excluded: chain Z residue 28 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 0.0770 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 ASN X 35 GLN X 292 ASN Y 88 ASN Y 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.139517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106398 restraints weight = 9576.196| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.98 r_work: 0.3072 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8338 Z= 0.135 Angle : 0.502 6.329 11291 Z= 0.266 Chirality : 0.042 0.183 1285 Planarity : 0.004 0.054 1436 Dihedral : 4.847 88.616 1129 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.38 % Allowed : 14.88 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 1020 helix: 1.71 (0.27), residues: 387 sheet: -0.78 (0.33), residues: 223 loop : -0.26 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 169 HIS 0.003 0.001 HIS X 357 PHE 0.016 0.001 PHE A 155 TYR 0.017 0.001 TYR A 197 ARG 0.004 0.000 ARG Y 219 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 444) hydrogen bonds : angle 5.21808 ( 1278) SS BOND : bond 0.00268 ( 2) SS BOND : angle 0.43870 ( 4) covalent geometry : bond 0.00310 ( 8336) covalent geometry : angle 0.50246 (11287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.8059 (mmm) cc_final: 0.7557 (tpp) REVERT: A 145 ILE cc_start: 0.7988 (mm) cc_final: 0.7756 (mt) REVERT: A 177 TYR cc_start: 0.9083 (p90) cc_final: 0.8882 (p90) REVERT: A 190 ASP cc_start: 0.7511 (t70) cc_final: 0.7037 (t0) REVERT: A 275 MET cc_start: 0.8387 (ttm) cc_final: 0.8174 (ttm) REVERT: N 80 TYR cc_start: 0.8394 (m-80) cc_final: 0.7906 (m-80) REVERT: Y 25 CYS cc_start: 0.7218 (t) cc_final: 0.6967 (t) REVERT: Y 43 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7954 (mt) REVERT: Y 59 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: Z 31 SER cc_start: 0.7553 (m) cc_final: 0.7338 (m) outliers start: 30 outliers final: 21 residues processed: 131 average time/residue: 0.2728 time to fit residues: 47.2783 Evaluate side-chains 134 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 292 ASN Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Y residue 228 ASP Chi-restraints excluded: chain Y residue 275 SER Chi-restraints excluded: chain Y residue 276 VAL Chi-restraints excluded: chain Z residue 28 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN X 35 GLN X 292 ASN Y 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.141143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.108201 restraints weight = 9622.829| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.99 r_work: 0.3089 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8338 Z= 0.139 Angle : 0.507 6.772 11291 Z= 0.268 Chirality : 0.042 0.147 1285 Planarity : 0.004 0.054 1436 Dihedral : 4.825 89.133 1129 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.16 % Allowed : 15.45 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.27), residues: 1020 helix: 1.74 (0.27), residues: 387 sheet: -0.75 (0.33), residues: 223 loop : -0.25 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Y 169 HIS 0.003 0.001 HIS X 357 PHE 0.015 0.001 PHE A 155 TYR 0.016 0.001 TYR A 197 ARG 0.004 0.000 ARG Y 19 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 444) hydrogen bonds : angle 5.16591 ( 1278) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.41144 ( 4) covalent geometry : bond 0.00322 ( 8336) covalent geometry : angle 0.50708 (11287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.8095 (mmm) cc_final: 0.7588 (tpp) REVERT: A 145 ILE cc_start: 0.8033 (mm) cc_final: 0.7817 (mt) REVERT: A 190 ASP cc_start: 0.7521 (t70) cc_final: 0.7039 (t0) REVERT: A 275 MET cc_start: 0.8401 (ttm) cc_final: 0.8105 (ttm) REVERT: N 80 TYR cc_start: 0.8430 (m-80) cc_final: 0.7912 (m-80) REVERT: Y 25 CYS cc_start: 0.7222 (t) cc_final: 0.6977 (t) REVERT: Y 43 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7952 (mt) REVERT: Y 59 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: Y 303 ASP cc_start: 0.7968 (m-30) cc_final: 0.7691 (m-30) REVERT: Z 31 SER cc_start: 0.7587 (m) cc_final: 0.7372 (m) outliers start: 28 outliers final: 23 residues processed: 129 average time/residue: 0.2404 time to fit residues: 41.1525 Evaluate side-chains 133 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 292 ASN Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Y residue 228 ASP Chi-restraints excluded: chain Y residue 234 PHE Chi-restraints excluded: chain Y residue 276 VAL Chi-restraints excluded: chain Z residue 28 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN X 35 GLN X 292 ASN Y 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.142025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.109236 restraints weight = 9678.437| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.99 r_work: 0.3070 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8338 Z= 0.140 Angle : 0.507 6.816 11291 Z= 0.267 Chirality : 0.042 0.176 1285 Planarity : 0.004 0.054 1436 Dihedral : 4.806 88.930 1129 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.93 % Allowed : 15.45 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.27), residues: 1020 helix: 1.66 (0.27), residues: 392 sheet: -0.68 (0.33), residues: 220 loop : -0.30 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 211 HIS 0.003 0.001 HIS X 357 PHE 0.014 0.001 PHE A 155 TYR 0.017 0.001 TYR A 197 ARG 0.004 0.000 ARG Y 19 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 444) hydrogen bonds : angle 5.14364 ( 1278) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.40643 ( 4) covalent geometry : bond 0.00324 ( 8336) covalent geometry : angle 0.50664 (11287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.8055 (mmm) cc_final: 0.7543 (tpp) REVERT: A 145 ILE cc_start: 0.7993 (mm) cc_final: 0.7772 (mt) REVERT: A 190 ASP cc_start: 0.7537 (t70) cc_final: 0.7041 (t0) REVERT: A 275 MET cc_start: 0.8368 (ttm) cc_final: 0.8076 (ttm) REVERT: N 80 TYR cc_start: 0.8408 (m-80) cc_final: 0.7887 (m-80) REVERT: Y 25 CYS cc_start: 0.7199 (t) cc_final: 0.6946 (t) REVERT: Y 43 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7926 (mt) REVERT: Y 59 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: Y 303 ASP cc_start: 0.7951 (m-30) cc_final: 0.7658 (m-30) REVERT: Z 31 SER cc_start: 0.7531 (m) cc_final: 0.7320 (m) outliers start: 26 outliers final: 22 residues processed: 127 average time/residue: 0.2682 time to fit residues: 45.2374 Evaluate side-chains 135 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 292 ASN Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Y residue 228 ASP Chi-restraints excluded: chain Y residue 234 PHE Chi-restraints excluded: chain Y residue 275 SER Chi-restraints excluded: chain Y residue 276 VAL Chi-restraints excluded: chain Z residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 4 optimal weight: 0.0770 chunk 64 optimal weight: 9.9990 chunk 55 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 83 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 35 GLN X 292 ASN Y 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.143564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111091 restraints weight = 9522.962| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.98 r_work: 0.3125 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8338 Z= 0.108 Angle : 0.485 6.477 11291 Z= 0.256 Chirality : 0.041 0.166 1285 Planarity : 0.004 0.055 1436 Dihedral : 4.703 88.646 1129 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.59 % Allowed : 15.90 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.27), residues: 1020 helix: 1.86 (0.27), residues: 387 sheet: -0.64 (0.33), residues: 217 loop : -0.25 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 169 HIS 0.003 0.000 HIS X 357 PHE 0.015 0.001 PHE A 155 TYR 0.015 0.001 TYR A 197 ARG 0.004 0.000 ARG Y 19 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 444) hydrogen bonds : angle 5.01137 ( 1278) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.37333 ( 4) covalent geometry : bond 0.00238 ( 8336) covalent geometry : angle 0.48456 (11287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.831 Fit side-chains REVERT: A 46 PHE cc_start: 0.7856 (t80) cc_final: 0.7640 (t80) REVERT: A 77 MET cc_start: 0.8046 (mmm) cc_final: 0.7516 (tpp) REVERT: A 145 ILE cc_start: 0.8001 (mm) cc_final: 0.7791 (mt) REVERT: A 190 ASP cc_start: 0.7511 (t70) cc_final: 0.7010 (t0) REVERT: A 275 MET cc_start: 0.8314 (ttm) cc_final: 0.8111 (ttm) REVERT: N 32 TYR cc_start: 0.8862 (m-80) cc_final: 0.8560 (m-80) REVERT: N 80 TYR cc_start: 0.8297 (m-80) cc_final: 0.7795 (m-80) REVERT: N 105 ARG cc_start: 0.7177 (ptm160) cc_final: 0.6574 (ptt90) REVERT: Y 25 CYS cc_start: 0.7121 (t) cc_final: 0.6865 (t) REVERT: Y 43 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7818 (mt) REVERT: Y 59 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: Y 212 ASP cc_start: 0.7545 (t70) cc_final: 0.7279 (t0) REVERT: Y 303 ASP cc_start: 0.7927 (m-30) cc_final: 0.7615 (m-30) REVERT: Z 31 SER cc_start: 0.7533 (m) cc_final: 0.7322 (m) outliers start: 23 outliers final: 19 residues processed: 126 average time/residue: 0.2273 time to fit residues: 38.7786 Evaluate side-chains 129 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 292 ASN Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 177 THR Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 228 ASP Chi-restraints excluded: chain Y residue 275 SER Chi-restraints excluded: chain Y residue 276 VAL Chi-restraints excluded: chain Z residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 40 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 38 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 5 optimal weight: 0.0370 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN X 35 GLN X 292 ASN Y 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109786 restraints weight = 9584.990| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.97 r_work: 0.3120 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8338 Z= 0.150 Angle : 0.512 6.977 11291 Z= 0.269 Chirality : 0.042 0.159 1285 Planarity : 0.004 0.053 1436 Dihedral : 4.786 89.369 1129 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.04 % Allowed : 15.56 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.27), residues: 1020 helix: 1.71 (0.27), residues: 393 sheet: -0.60 (0.33), residues: 219 loop : -0.28 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 211 HIS 0.003 0.001 HIS X 357 PHE 0.013 0.001 PHE A 155 TYR 0.020 0.002 TYR A 34 ARG 0.005 0.000 ARG X 356 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 444) hydrogen bonds : angle 5.10959 ( 1278) SS BOND : bond 0.00210 ( 2) SS BOND : angle 0.37183 ( 4) covalent geometry : bond 0.00352 ( 8336) covalent geometry : angle 0.51225 (11287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5193.66 seconds wall clock time: 91 minutes 23.11 seconds (5483.11 seconds total)