Starting phenix.real_space_refine on Sat Dec 28 08:24:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f76_28896/12_2024/8f76_28896.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f76_28896/12_2024/8f76_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_28896/12_2024/8f76_28896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f76_28896/12_2024/8f76_28896.map" model { file = "/net/cci-nas-00/data/ceres_data/8f76_28896/12_2024/8f76_28896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f76_28896/12_2024/8f76_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-5532/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: 5.45, per 1000 atoms: 0.67 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: 1.99 Conformation dependent library (CDL) restraints added in 1.1 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: 0.97 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: 2.36 Time building geometry restraints manager: 2.23 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.480 Find NCS groups from input model: 0.080 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.480 ------------------------------------------------------------------------------- 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 8336 Z= 0.308 Angle : 0.854 10.521 11287 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 *********************** 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 : 0.884 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: 0.2518 time to fit residues: 37.9810 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 : 0.781 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 8336 Z= 0.416 Angle : 0.640 8.488 11287 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 *********************** 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 : 0.919 Fit side-chains revert: symmetry clash REVERT: A 190 ASP cc_start: 0.7021 (t70) cc_final: 0.6802 (t0) REVERT: Z 31 SER cc_start: 0.7997 (m) cc_final: 0.7736 (m) outliers start: 8 outliers final: 4 residues processed: 125 average time/residue: 0.2571 time to fit residues: 41.8578 Evaluate side-chains 110 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 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** X 35 GLN X 292 ASN Y 32 GLN Y 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8336 Z= 0.202 Angle : 0.521 5.939 11287 Z= 0.276 Chirality : 0.042 0.142 1285 Planarity : 0.004 0.059 1436 Dihedral : 5.058 89.809 1129 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.48 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: 0.17 (0.26), residues: 1020 helix: 1.28 (0.26), residues: 386 sheet: -0.72 (0.34), residues: 214 loop : -0.40 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 A 197 ARG 0.007 0.000 ARG Y 219 *********************** 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 127 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 190 ASP cc_start: 0.6995 (t70) cc_final: 0.6793 (t0) REVERT: N 80 TYR cc_start: 0.8058 (m-80) cc_final: 0.7853 (m-80) REVERT: X 220 HIS cc_start: 0.8176 (t-170) cc_final: 0.7740 (t-90) REVERT: Z 31 SER cc_start: 0.7943 (m) cc_final: 0.7709 (m) outliers start: 15 outliers final: 11 residues processed: 120 average time/residue: 0.2635 time to fit residues: 41.6509 Evaluate side-chains 116 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 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 186 ASP 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 69 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8336 Z= 0.262 Angle : 0.532 6.833 11287 Z= 0.280 Chirality : 0.043 0.164 1285 Planarity : 0.004 0.056 1436 Dihedral : 4.982 88.932 1129 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.71 % Allowed : 11.72 % Favored : 85.57 % 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 (0.27), residues: 1020 helix: 1.42 (0.27), residues: 387 sheet: -0.85 (0.34), residues: 222 loop : -0.30 (0.31), residues: 411 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 0.019 0.002 TYR A 197 ARG 0.004 0.000 ARG Y 219 *********************** 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 134 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 190 ASP cc_start: 0.7049 (t70) cc_final: 0.6800 (t0) REVERT: N 80 TYR cc_start: 0.8208 (m-80) cc_final: 0.7884 (m-80) REVERT: X 220 HIS cc_start: 0.8176 (t-170) cc_final: 0.7708 (t-90) REVERT: Y 43 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7980 (mt) REVERT: Z 31 SER cc_start: 0.7922 (m) cc_final: 0.7675 (m) outliers start: 24 outliers final: 19 residues processed: 125 average time/residue: 0.2392 time to fit residues: 39.6342 Evaluate side-chains 126 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8336 Z= 0.227 Angle : 0.512 6.555 11287 Z= 0.271 Chirality : 0.042 0.172 1285 Planarity : 0.004 0.056 1436 Dihedral : 4.923 89.917 1129 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.16 % Allowed : 13.53 % Favored : 83.31 % 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: 0.38 (0.27), residues: 1020 helix: 1.59 (0.27), residues: 386 sheet: -0.82 (0.33), residues: 218 loop : -0.30 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 211 HIS 0.004 0.001 HIS X 220 PHE 0.016 0.001 PHE A 155 TYR 0.017 0.001 TYR A 197 ARG 0.003 0.000 ARG Y 219 *********************** 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 142 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 190 ASP cc_start: 0.7043 (t70) cc_final: 0.6792 (t0) REVERT: Y 43 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7978 (mt) REVERT: Y 59 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.8079 (m-80) REVERT: Y 333 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7330 (m-30) REVERT: Z 31 SER cc_start: 0.7912 (m) cc_final: 0.7672 (m) outliers start: 28 outliers final: 20 residues processed: 131 average time/residue: 0.2367 time to fit residues: 40.9520 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 : 0.959 ------------------------------------------------------------------------------- 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 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 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 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 Y residue 333 ASP 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 87 optimal weight: 0.0270 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8336 Z= 0.178 Angle : 0.490 6.526 11287 Z= 0.259 Chirality : 0.041 0.147 1285 Planarity : 0.004 0.055 1436 Dihedral : 4.827 89.817 1129 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.16 % Allowed : 14.66 % Favored : 82.19 % 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: 0.46 (0.27), residues: 1020 helix: 1.69 (0.27), residues: 389 sheet: -0.75 (0.33), residues: 218 loop : -0.33 (0.31), residues: 413 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 0.003 0.000 ARG Y 19 *********************** 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 138 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 190 ASP cc_start: 0.7043 (t70) cc_final: 0.6776 (t0) REVERT: Y 59 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.8029 (m-80) REVERT: Z 31 SER cc_start: 0.7910 (m) cc_final: 0.7664 (m) outliers start: 28 outliers final: 21 residues processed: 127 average time/residue: 0.2491 time to fit residues: 41.4729 Evaluate side-chains 130 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 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 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 11 optimal weight: 0.9980 chunk 55 optimal weight: 0.0000 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8336 Z= 0.198 Angle : 0.495 6.776 11287 Z= 0.261 Chirality : 0.042 0.167 1285 Planarity : 0.004 0.055 1436 Dihedral : 4.800 89.836 1129 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.38 % Allowed : 14.77 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.27), residues: 1020 helix: 1.77 (0.27), residues: 389 sheet: -0.79 (0.33), residues: 225 loop : -0.31 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 211 HIS 0.003 0.001 HIS X 220 PHE 0.015 0.001 PHE A 155 TYR 0.016 0.001 TYR A 197 ARG 0.004 0.000 ARG Y 19 *********************** 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 140 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.926 Fit side-chains REVERT: A 190 ASP cc_start: 0.7024 (t70) cc_final: 0.6809 (t0) REVERT: A 206 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7215 (mtm) REVERT: X 220 HIS cc_start: 0.8067 (t-90) cc_final: 0.7674 (t-90) REVERT: Y 43 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7880 (mt) REVERT: Y 59 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: Z 31 SER cc_start: 0.7914 (m) cc_final: 0.7664 (m) outliers start: 30 outliers final: 24 residues processed: 128 average time/residue: 0.2316 time to fit residues: 39.8777 Evaluate side-chains 137 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 206 MET 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 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 Y residue 333 ASP 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 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 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 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8336 Z= 0.202 Angle : 0.497 6.758 11287 Z= 0.263 Chirality : 0.042 0.149 1285 Planarity : 0.004 0.054 1436 Dihedral : 4.787 89.692 1129 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.27 % Allowed : 14.88 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.27), residues: 1020 helix: 1.80 (0.27), residues: 389 sheet: -0.77 (0.33), residues: 225 loop : -0.32 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Y 169 HIS 0.003 0.001 HIS X 220 PHE 0.015 0.001 PHE A 155 TYR 0.015 0.001 TYR A 197 ARG 0.004 0.000 ARG Y 19 *********************** 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 142 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.913 Fit side-chains REVERT: A 77 MET cc_start: 0.8050 (mmm) cc_final: 0.7632 (tpp) REVERT: A 190 ASP cc_start: 0.7009 (t70) cc_final: 0.6776 (t0) REVERT: A 206 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7216 (mtm) REVERT: X 220 HIS cc_start: 0.8041 (t-90) cc_final: 0.7659 (t-90) REVERT: Y 43 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7864 (mt) REVERT: Y 59 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: Y 219 ARG cc_start: 0.7601 (mtt-85) cc_final: 0.7272 (tpp80) REVERT: Z 31 SER cc_start: 0.7915 (m) cc_final: 0.7691 (m) outliers start: 29 outliers final: 24 residues processed: 129 average time/residue: 0.2366 time to fit residues: 40.6211 Evaluate side-chains 135 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 206 MET 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 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 Y residue 333 ASP 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 90 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 95 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8336 Z= 0.278 Angle : 0.535 7.149 11287 Z= 0.281 Chirality : 0.043 0.163 1285 Planarity : 0.004 0.053 1436 Dihedral : 4.889 89.559 1129 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.27 % Allowed : 14.77 % Favored : 81.96 % 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: 0.46 (0.27), residues: 1020 helix: 1.73 (0.27), residues: 387 sheet: -0.79 (0.33), residues: 225 loop : -0.31 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 211 HIS 0.004 0.001 HIS X 220 PHE 0.015 0.001 PHE X 212 TYR 0.017 0.002 TYR A 197 ARG 0.004 0.000 ARG Y 19 *********************** 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 141 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.8038 (mmm) cc_final: 0.7622 (tpp) REVERT: A 190 ASP cc_start: 0.7006 (t70) cc_final: 0.6778 (t0) REVERT: A 206 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7368 (mtm) REVERT: N 80 TYR cc_start: 0.8349 (m-80) cc_final: 0.7911 (m-80) REVERT: Y 43 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7973 (mt) REVERT: Y 59 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.8074 (m-80) REVERT: Y 219 ARG cc_start: 0.7662 (mtt-85) cc_final: 0.7336 (tpp80) REVERT: Y 303 ASP cc_start: 0.7412 (m-30) cc_final: 0.7182 (m-30) REVERT: Z 31 SER cc_start: 0.7924 (m) cc_final: 0.7683 (m) outliers start: 29 outliers final: 24 residues processed: 128 average time/residue: 0.2521 time to fit residues: 42.2191 Evaluate side-chains 138 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 206 MET 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 122 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP 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 Y residue 333 ASP 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 45 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 35 GLN ** X 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8336 Z= 0.169 Angle : 0.492 6.433 11287 Z= 0.260 Chirality : 0.041 0.156 1285 Planarity : 0.004 0.055 1436 Dihedral : 4.781 89.677 1129 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.27 % Allowed : 15.11 % 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: 0.60 (0.27), residues: 1020 helix: 1.84 (0.27), residues: 388 sheet: -0.65 (0.33), residues: 222 loop : -0.29 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 169 HIS 0.003 0.001 HIS X 357 PHE 0.016 0.001 PHE A 155 TYR 0.015 0.001 TYR A 197 ARG 0.004 0.000 ARG Y 19 ********************** 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 138 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.552 Fit side-chains REVERT: A 77 MET cc_start: 0.8036 (mmm) cc_final: 0.7600 (tpp) REVERT: A 190 ASP cc_start: 0.6951 (t70) cc_final: 0.6715 (t0) REVERT: N 80 TYR cc_start: 0.8201 (m-80) cc_final: 0.7832 (m-80) REVERT: Y 43 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7779 (mt) REVERT: Y 59 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: Y 219 ARG cc_start: 0.7588 (mtt-85) cc_final: 0.7272 (tpp80) REVERT: Y 303 ASP cc_start: 0.7395 (m-30) cc_final: 0.7149 (m-30) REVERT: Z 31 SER cc_start: 0.7938 (m) cc_final: 0.7697 (m) outliers start: 29 outliers final: 22 residues processed: 124 average time/residue: 0.2650 time to fit residues: 43.9983 Evaluate side-chains 131 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP 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 234 PHE Chi-restraints excluded: chain Y residue 275 SER Chi-restraints excluded: chain Y residue 276 VAL Chi-restraints excluded: chain Y residue 333 ASP 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 73 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111708 restraints weight = 9407.941| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.93 r_work: 0.3114 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8336 Z= 0.181 Angle : 0.499 6.796 11287 Z= 0.262 Chirality : 0.042 0.155 1285 Planarity : 0.004 0.055 1436 Dihedral : 4.679 84.402 1129 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.93 % Allowed : 15.33 % 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: 0.67 (0.27), residues: 1020 helix: 1.91 (0.27), residues: 387 sheet: -0.62 (0.33), residues: 221 loop : -0.27 (0.32), residues: 412 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 0.014 0.001 PHE A 155 TYR 0.019 0.001 TYR A 34 ARG 0.004 0.000 ARG Y 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2099.58 seconds wall clock time: 39 minutes 2.92 seconds (2342.92 seconds total)