Starting phenix.real_space_refine on Wed Sep 17 08:24:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k25_61990/09_2025/9k25_61990.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k25_61990/09_2025/9k25_61990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k25_61990/09_2025/9k25_61990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k25_61990/09_2025/9k25_61990.map" model { file = "/net/cci-nas-00/data/ceres_data/9k25_61990/09_2025/9k25_61990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k25_61990/09_2025/9k25_61990.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.076 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 48 5.16 5 C 4568 2.51 5 N 1232 2.21 5 O 1269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7117 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1634 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 207} Chain breaks: 3 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2258 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 7, 'GLN:plan1': 5, 'ARG:plan': 9, 'ASP:plan': 16, 'TYR:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 172 Chain: "G" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 227 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "I" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2107 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 5, 'PHE:plan': 4, 'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 83 Chain: "N" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 891 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 1.84, per 1000 atoms: 0.26 Number of scatterers: 7117 At special positions: 0 Unit cell: (75.6, 98.28, 127.44, 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 48 16.00 O 1269 8.00 N 1232 7.00 C 4568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 278 " distance=1.88 Simple disulfide: pdb=" SG CYS I 106 " - pdb=" SG CYS I 183 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 363.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 10 sheets defined 40.1% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.786A pdb=" N ALA A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 278 removed outlier: 4.093A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.562A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 333 through 352 removed outlier: 4.533A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 15 through 24 removed outlier: 3.953A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.577A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 25 Processing helix chain 'I' and resid 29 through 61 Proline residue: I 37 - end of helix Processing helix chain 'I' and resid 66 through 95 removed outlier: 4.299A pdb=" N SER I 78 " --> pdb=" O HIS I 74 " (cutoff:3.500A) Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 102 through 137 removed outlier: 3.552A pdb=" N ARG I 137 " --> pdb=" O LEU I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 144 removed outlier: 3.516A pdb=" N TRP I 144 " --> pdb=" O ARG I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 165 Processing helix chain 'I' and resid 165 through 172 Processing helix chain 'I' and resid 191 through 207 Processing helix chain 'I' and resid 207 through 227 Processing helix chain 'I' and resid 240 through 270 Proline residue: I 260 - end of helix removed outlier: 3.623A pdb=" N THR I 266 " --> pdb=" O HIS I 262 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER I 270 " --> pdb=" O THR I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 308 removed outlier: 3.637A pdb=" N ALA I 283 " --> pdb=" O HIS I 279 " (cutoff:3.500A) Proline residue: I 293 - end of helix removed outlier: 4.529A pdb=" N ASN I 298 " --> pdb=" O LEU I 294 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER I 299 " --> pdb=" O ALA I 295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS I 300 " --> pdb=" O SER I 296 " (cutoff:3.500A) Proline residue: I 303 - end of helix Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.779A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 7.192A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.501A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.901A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.761A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 180 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.664A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.555A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 277 Processing sheet with id=AA9, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.591A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP N 73 " --> pdb=" O THR N 78 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 34 through 39 removed outlier: 3.823A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 0.81 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: 2279 1.34 - 1.46: 1868 1.46 - 1.59: 3060 1.59 - 1.71: 0 1.71 - 1.83: 61 Bond restraints: 7268 Sorted by residual: bond pdb=" CA SER I 277 " pdb=" C SER I 277 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.29e-02 6.01e+03 7.38e+00 bond pdb=" CA ARG I 26 " pdb=" C ARG I 26 " ideal model delta sigma weight residual 1.527 1.493 0.034 1.30e-02 5.92e+03 7.02e+00 bond pdb=" N LEU A 12 " pdb=" CA LEU A 12 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.30e+00 bond pdb=" CA LEU I 276 " pdb=" C LEU I 276 " ideal model delta sigma weight residual 1.521 1.548 -0.027 1.54e-02 4.22e+03 3.15e+00 bond pdb=" C ARG I 26 " pdb=" N PHE I 27 " ideal model delta sigma weight residual 1.333 1.310 0.024 1.34e-02 5.57e+03 3.11e+00 ... (remaining 7263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 9607 1.53 - 3.07: 261 3.07 - 4.60: 49 4.60 - 6.14: 10 6.14 - 7.67: 1 Bond angle restraints: 9928 Sorted by residual: angle pdb=" N ASP I 19 " pdb=" CA ASP I 19 " pdb=" C ASP I 19 " ideal model delta sigma weight residual 111.07 107.30 3.77 1.07e+00 8.73e-01 1.24e+01 angle pdb=" N HIS I 184 " pdb=" CA HIS I 184 " pdb=" C HIS I 184 " ideal model delta sigma weight residual 110.10 115.25 -5.15 1.49e+00 4.50e-01 1.20e+01 angle pdb=" N ASN I 282 " pdb=" CA ASN I 282 " pdb=" C ASN I 282 " ideal model delta sigma weight residual 111.28 107.66 3.62 1.09e+00 8.42e-01 1.11e+01 angle pdb=" N ASP I 30 " pdb=" CA ASP I 30 " pdb=" C ASP I 30 " ideal model delta sigma weight residual 111.71 108.47 3.24 1.15e+00 7.56e-01 7.95e+00 angle pdb=" C ILE I 284 " pdb=" CA ILE I 284 " pdb=" CB ILE I 284 " ideal model delta sigma weight residual 112.14 108.38 3.76 1.35e+00 5.49e-01 7.77e+00 ... (remaining 9923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 3672 16.87 - 33.74: 408 33.74 - 50.61: 121 50.61 - 67.48: 17 67.48 - 84.35: 6 Dihedral angle restraints: 4224 sinusoidal: 1374 harmonic: 2850 Sorted by residual: dihedral pdb=" CA ASN A 292 " pdb=" C ASN A 292 " pdb=" N LYS A 293 " pdb=" CA LYS A 293 " ideal model delta harmonic sigma weight residual -180.00 -161.27 -18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ALA N 56 " pdb=" C ALA N 56 " pdb=" N SER N 57 " pdb=" CA SER N 57 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASP B 118 " pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 4221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 835 0.037 - 0.073: 244 0.073 - 0.110: 83 0.110 - 0.146: 25 0.146 - 0.183: 1 Chirality restraints: 1188 Sorted by residual: chirality pdb=" CG LEU I 276 " pdb=" CB LEU I 276 " pdb=" CD1 LEU I 276 " pdb=" CD2 LEU I 276 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CA VAL N 93 " pdb=" N VAL N 93 " pdb=" C VAL N 93 " pdb=" CB VAL N 93 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1185 not shown) Planarity restraints: 1244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 158 " -0.018 2.00e-02 2.50e+03 1.52e-02 5.74e+00 pdb=" CG TRP I 158 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP I 158 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP I 158 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP I 158 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP I 158 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 158 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 158 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 158 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP I 158 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR I 23 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.37e+00 pdb=" C TYR I 23 " 0.032 2.00e-02 2.50e+03 pdb=" O TYR I 23 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG I 24 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 209 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO I 210 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO I 210 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 210 " -0.025 5.00e-02 4.00e+02 ... (remaining 1241 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 829 2.74 - 3.28: 7207 3.28 - 3.82: 11930 3.82 - 4.36: 13522 4.36 - 4.90: 24317 Nonbonded interactions: 57805 Sorted by model distance: nonbonded pdb=" O PRO I 260 " pdb=" OG1 THR I 264 " model vdw 2.206 3.040 nonbonded pdb=" O LYS B 57 " pdb=" OG SER B 74 " model vdw 2.207 3.040 nonbonded pdb=" NH2 ARG A 231 " pdb=" OD2 ASP A 272 " model vdw 2.244 3.120 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.257 3.040 nonbonded pdb=" OE1 GLN A 267 " pdb=" ND2 ASN A 271 " model vdw 2.297 3.120 ... (remaining 57800 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: 1.390 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.110 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 : 0.004 0.150 7271 Z= 0.209 Angle : 0.638 7.672 9934 Z= 0.362 Chirality : 0.041 0.183 1188 Planarity : 0.004 0.052 1244 Dihedral : 15.933 84.350 2371 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 27.70 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.27), residues: 954 helix: 0.83 (0.27), residues: 369 sheet: -1.71 (0.37), residues: 189 loop : -2.11 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 22 TYR 0.015 0.001 TYR I 218 PHE 0.012 0.001 PHE B 234 TRP 0.037 0.002 TRP I 158 HIS 0.015 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7268) covalent geometry : angle 0.63568 ( 9928) SS BOND : bond 0.08684 ( 3) SS BOND : angle 2.41826 ( 6) hydrogen bonds : bond 0.17128 ( 360) hydrogen bonds : angle 7.12177 ( 1035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.259 Fit side-chains REVERT: A 311 TYR cc_start: 0.7208 (m-80) cc_final: 0.6974 (m-80) REVERT: B 219 ARG cc_start: 0.7437 (mtm180) cc_final: 0.7172 (mtt180) REVERT: B 339 TRP cc_start: 0.8518 (m100) cc_final: 0.8280 (m-10) REVERT: I 72 MET cc_start: 0.7474 (mtt) cc_final: 0.7119 (mtt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0978 time to fit residues: 15.7808 Evaluate side-chains 110 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0170 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.187629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.152186 restraints weight = 8823.462| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.23 r_work: 0.3793 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7271 Z= 0.135 Angle : 0.563 6.081 9934 Z= 0.298 Chirality : 0.042 0.166 1188 Planarity : 0.004 0.036 1244 Dihedral : 4.360 18.105 1052 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.89 % Allowed : 24.15 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.27), residues: 954 helix: 1.27 (0.27), residues: 374 sheet: -1.40 (0.37), residues: 188 loop : -2.01 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.012 0.001 TYR I 33 PHE 0.013 0.001 PHE B 199 TRP 0.013 0.002 TRP I 158 HIS 0.010 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7268) covalent geometry : angle 0.56267 ( 9928) SS BOND : bond 0.00380 ( 3) SS BOND : angle 0.59468 ( 6) hydrogen bonds : bond 0.04176 ( 360) hydrogen bonds : angle 5.24053 ( 1035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: A 392 ASN cc_start: 0.7999 (t0) cc_final: 0.7588 (p0) REVERT: B 234 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7189 (m-80) REVERT: I 33 TYR cc_start: 0.6481 (m-80) cc_final: 0.6278 (m-80) REVERT: N 82 GLN cc_start: 0.8211 (tp-100) cc_final: 0.7913 (tp40) outliers start: 33 outliers final: 17 residues processed: 141 average time/residue: 0.0755 time to fit residues: 14.9549 Evaluate side-chains 132 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 78 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 2 optimal weight: 0.0010 chunk 58 optimal weight: 0.2980 chunk 60 optimal weight: 5.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.182553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.148074 restraints weight = 8649.897| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.20 r_work: 0.3823 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7271 Z= 0.117 Angle : 0.534 5.407 9934 Z= 0.282 Chirality : 0.042 0.152 1188 Planarity : 0.004 0.037 1244 Dihedral : 4.155 17.850 1052 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.04 % Allowed : 26.52 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.27), residues: 954 helix: 1.52 (0.27), residues: 374 sheet: -1.50 (0.33), residues: 211 loop : -2.00 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 22 TYR 0.012 0.001 TYR I 92 PHE 0.011 0.001 PHE I 207 TRP 0.014 0.001 TRP I 158 HIS 0.004 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7268) covalent geometry : angle 0.53367 ( 9928) SS BOND : bond 0.00286 ( 3) SS BOND : angle 0.62466 ( 6) hydrogen bonds : bond 0.03734 ( 360) hydrogen bonds : angle 4.83487 ( 1035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.265 Fit side-chains REVERT: A 267 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: A 392 ASN cc_start: 0.8021 (t0) cc_final: 0.7560 (p0) REVERT: B 200 VAL cc_start: 0.8752 (m) cc_final: 0.8518 (p) REVERT: B 234 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7407 (m-80) REVERT: I 72 MET cc_start: 0.7899 (mtt) cc_final: 0.7418 (mtt) REVERT: N 82 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7941 (tp40) outliers start: 34 outliers final: 22 residues processed: 144 average time/residue: 0.0808 time to fit residues: 15.8381 Evaluate side-chains 138 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.0670 chunk 94 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.182093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147441 restraints weight = 8718.005| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.21 r_work: 0.3817 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7271 Z= 0.121 Angle : 0.535 6.943 9934 Z= 0.280 Chirality : 0.042 0.158 1188 Planarity : 0.004 0.037 1244 Dihedral : 4.077 18.409 1052 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.93 % Allowed : 25.78 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.27), residues: 954 helix: 1.63 (0.27), residues: 371 sheet: -1.45 (0.33), residues: 209 loop : -1.94 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 22 TYR 0.012 0.001 TYR I 92 PHE 0.011 0.001 PHE I 207 TRP 0.020 0.001 TRP B 339 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7268) covalent geometry : angle 0.53544 ( 9928) SS BOND : bond 0.00277 ( 3) SS BOND : angle 0.61488 ( 6) hydrogen bonds : bond 0.03584 ( 360) hydrogen bonds : angle 4.64291 ( 1035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.259 Fit side-chains REVERT: A 267 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: A 392 ASN cc_start: 0.7938 (t0) cc_final: 0.7552 (p0) REVERT: B 234 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7508 (m-80) REVERT: I 72 MET cc_start: 0.7846 (mtt) cc_final: 0.7431 (mtt) REVERT: I 79 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7701 (t0) REVERT: N 82 GLN cc_start: 0.8097 (tp-100) cc_final: 0.7767 (tp40) outliers start: 40 outliers final: 25 residues processed: 146 average time/residue: 0.0684 time to fit residues: 14.1447 Evaluate side-chains 147 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.177400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141299 restraints weight = 8719.480| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.25 r_work: 0.3754 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7271 Z= 0.131 Angle : 0.541 6.575 9934 Z= 0.282 Chirality : 0.042 0.215 1188 Planarity : 0.004 0.038 1244 Dihedral : 4.073 18.497 1052 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.63 % Allowed : 26.07 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.27), residues: 954 helix: 1.60 (0.27), residues: 372 sheet: -1.50 (0.33), residues: 211 loop : -1.97 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 22 TYR 0.012 0.001 TYR N 60 PHE 0.014 0.001 PHE B 199 TRP 0.023 0.002 TRP B 339 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7268) covalent geometry : angle 0.54055 ( 9928) SS BOND : bond 0.00302 ( 3) SS BOND : angle 0.70433 ( 6) hydrogen bonds : bond 0.03567 ( 360) hydrogen bonds : angle 4.64310 ( 1035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.198 Fit side-chains REVERT: A 267 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: A 392 ASN cc_start: 0.8043 (t0) cc_final: 0.7579 (p0) REVERT: I 72 MET cc_start: 0.7954 (mtt) cc_final: 0.7541 (mtt) REVERT: I 79 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7759 (t0) REVERT: N 82 GLN cc_start: 0.8034 (tp-100) cc_final: 0.7623 (tp40) outliers start: 38 outliers final: 29 residues processed: 147 average time/residue: 0.0718 time to fit residues: 14.7723 Evaluate side-chains 150 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 66 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 82 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.176949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.140861 restraints weight = 8701.963| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.23 r_work: 0.3751 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7271 Z= 0.132 Angle : 0.540 6.882 9934 Z= 0.283 Chirality : 0.042 0.222 1188 Planarity : 0.004 0.038 1244 Dihedral : 4.057 18.768 1052 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 6.81 % Allowed : 25.19 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.27), residues: 954 helix: 1.60 (0.27), residues: 372 sheet: -1.52 (0.32), residues: 211 loop : -1.97 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 22 TYR 0.012 0.001 TYR N 60 PHE 0.015 0.001 PHE B 199 TRP 0.038 0.002 TRP B 339 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7268) covalent geometry : angle 0.53976 ( 9928) SS BOND : bond 0.00238 ( 3) SS BOND : angle 0.69698 ( 6) hydrogen bonds : bond 0.03550 ( 360) hydrogen bonds : angle 4.60394 ( 1035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.272 Fit side-chains REVERT: A 267 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: B 212 ASP cc_start: 0.8608 (t0) cc_final: 0.8354 (t0) REVERT: I 72 MET cc_start: 0.7864 (mtt) cc_final: 0.7441 (mtt) REVERT: I 79 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7806 (t0) REVERT: N 82 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7592 (tp40) outliers start: 46 outliers final: 30 residues processed: 154 average time/residue: 0.0704 time to fit residues: 15.1835 Evaluate side-chains 145 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.174335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.137885 restraints weight = 8764.006| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.25 r_work: 0.3678 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7271 Z= 0.182 Angle : 0.578 7.607 9934 Z= 0.305 Chirality : 0.044 0.202 1188 Planarity : 0.004 0.039 1244 Dihedral : 4.322 19.718 1052 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.07 % Allowed : 26.67 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.27), residues: 954 helix: 1.35 (0.27), residues: 378 sheet: -1.57 (0.32), residues: 204 loop : -1.99 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 22 TYR 0.017 0.001 TYR N 60 PHE 0.021 0.002 PHE B 199 TRP 0.036 0.002 TRP B 339 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 7268) covalent geometry : angle 0.57798 ( 9928) SS BOND : bond 0.00233 ( 3) SS BOND : angle 0.91628 ( 6) hydrogen bonds : bond 0.03854 ( 360) hydrogen bonds : angle 4.77052 ( 1035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.274 Fit side-chains REVERT: A 29 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8062 (mp10) REVERT: A 267 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: B 126 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7154 (pp) REVERT: B 234 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7718 (m-10) REVERT: I 72 MET cc_start: 0.7922 (mtt) cc_final: 0.7440 (mtt) REVERT: I 79 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7895 (t0) REVERT: N 58 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7434 (mp) REVERT: N 82 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7661 (tp40) outliers start: 41 outliers final: 27 residues processed: 146 average time/residue: 0.0734 time to fit residues: 15.1441 Evaluate side-chains 142 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.1980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.176383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.139890 restraints weight = 8807.243| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.24 r_work: 0.3742 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7271 Z= 0.134 Angle : 0.548 7.206 9934 Z= 0.288 Chirality : 0.042 0.180 1188 Planarity : 0.004 0.038 1244 Dihedral : 4.140 19.005 1052 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.93 % Allowed : 27.56 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.27), residues: 954 helix: 1.41 (0.27), residues: 378 sheet: -1.59 (0.31), residues: 221 loop : -2.00 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 22 TYR 0.012 0.001 TYR N 60 PHE 0.014 0.001 PHE B 199 TRP 0.031 0.002 TRP B 339 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7268) covalent geometry : angle 0.54810 ( 9928) SS BOND : bond 0.00240 ( 3) SS BOND : angle 0.71603 ( 6) hydrogen bonds : bond 0.03609 ( 360) hydrogen bonds : angle 4.66513 ( 1035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 0.283 Fit side-chains REVERT: A 29 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: A 267 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: B 339 TRP cc_start: 0.8565 (OUTLIER) cc_final: 0.8238 (m-10) REVERT: I 72 MET cc_start: 0.7903 (mtt) cc_final: 0.7462 (mtt) REVERT: I 79 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7854 (t0) REVERT: I 286 MET cc_start: 0.7750 (mmp) cc_final: 0.7446 (mmt) REVERT: N 58 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7373 (mp) REVERT: N 82 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7599 (tp40) outliers start: 40 outliers final: 28 residues processed: 146 average time/residue: 0.0741 time to fit residues: 15.1478 Evaluate side-chains 145 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 90 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 79 optimal weight: 0.2980 chunk 14 optimal weight: 0.0870 chunk 58 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.182261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.146761 restraints weight = 8670.023| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.26 r_work: 0.3804 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7271 Z= 0.104 Angle : 0.534 8.701 9934 Z= 0.275 Chirality : 0.041 0.171 1188 Planarity : 0.004 0.039 1244 Dihedral : 3.890 17.303 1052 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.19 % Allowed : 28.74 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.27), residues: 954 helix: 1.69 (0.27), residues: 375 sheet: -1.40 (0.32), residues: 221 loop : -1.85 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 22 TYR 0.013 0.001 TYR A 360 PHE 0.009 0.001 PHE I 207 TRP 0.029 0.002 TRP I 158 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7268) covalent geometry : angle 0.53377 ( 9928) SS BOND : bond 0.00250 ( 3) SS BOND : angle 0.54113 ( 6) hydrogen bonds : bond 0.03333 ( 360) hydrogen bonds : angle 4.49872 ( 1035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.254 Fit side-chains REVERT: A 223 ASP cc_start: 0.8190 (p0) cc_final: 0.7954 (p0) REVERT: A 267 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: A 381 ASP cc_start: 0.8460 (t70) cc_final: 0.8166 (t0) REVERT: B 125 ASN cc_start: 0.8543 (t0) cc_final: 0.8080 (p0) REVERT: I 72 MET cc_start: 0.7841 (mtt) cc_final: 0.7387 (mtt) REVERT: I 79 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7627 (t0) REVERT: I 221 MET cc_start: 0.6350 (mtp) cc_final: 0.6139 (mtp) REVERT: N 82 GLN cc_start: 0.7940 (tp-100) cc_final: 0.7496 (tp40) outliers start: 35 outliers final: 24 residues processed: 145 average time/residue: 0.0738 time to fit residues: 15.1532 Evaluate side-chains 135 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 14 optimal weight: 0.0470 chunk 21 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.178274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.142437 restraints weight = 8677.981| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.22 r_work: 0.3751 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7271 Z= 0.131 Angle : 0.555 8.202 9934 Z= 0.287 Chirality : 0.042 0.168 1188 Planarity : 0.004 0.037 1244 Dihedral : 3.982 18.104 1052 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.04 % Allowed : 29.33 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.27), residues: 954 helix: 1.50 (0.27), residues: 379 sheet: -1.35 (0.32), residues: 221 loop : -1.86 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 22 TYR 0.011 0.001 TYR N 60 PHE 0.013 0.001 PHE B 199 TRP 0.039 0.002 TRP I 158 HIS 0.003 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7268) covalent geometry : angle 0.55530 ( 9928) SS BOND : bond 0.00201 ( 3) SS BOND : angle 0.63384 ( 6) hydrogen bonds : bond 0.03448 ( 360) hydrogen bonds : angle 4.57296 ( 1035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.242 Fit side-chains REVERT: A 267 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: I 72 MET cc_start: 0.7996 (mtt) cc_final: 0.7569 (mtt) REVERT: I 79 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7831 (t0) REVERT: N 82 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7584 (tp40) outliers start: 34 outliers final: 28 residues processed: 136 average time/residue: 0.0718 time to fit residues: 13.8593 Evaluate side-chains 138 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 93 optimal weight: 0.0670 chunk 64 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 44 optimal weight: 0.0370 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 13 optimal weight: 0.0170 chunk 92 optimal weight: 3.9990 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.183578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.148786 restraints weight = 8676.014| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.21 r_work: 0.3826 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7271 Z= 0.104 Angle : 0.542 8.502 9934 Z= 0.277 Chirality : 0.041 0.171 1188 Planarity : 0.004 0.038 1244 Dihedral : 3.813 16.730 1052 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.59 % Allowed : 30.07 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.27), residues: 954 helix: 1.73 (0.27), residues: 376 sheet: -1.15 (0.33), residues: 216 loop : -1.78 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 22 TYR 0.009 0.001 TYR N 32 PHE 0.011 0.001 PHE I 111 TRP 0.038 0.002 TRP I 158 HIS 0.003 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 7268) covalent geometry : angle 0.54246 ( 9928) SS BOND : bond 0.00240 ( 3) SS BOND : angle 0.47390 ( 6) hydrogen bonds : bond 0.03238 ( 360) hydrogen bonds : angle 4.46049 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2092.12 seconds wall clock time: 36 minutes 35.98 seconds (2195.98 seconds total)