Starting phenix.real_space_refine on Wed Sep 17 09:06:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ima_60686/09_2025/9ima_60686.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ima_60686/09_2025/9ima_60686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ima_60686/09_2025/9ima_60686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ima_60686/09_2025/9ima_60686.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ima_60686/09_2025/9ima_60686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ima_60686/09_2025/9ima_60686.map" } resolution = 2.65 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= 0.030 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 51 5.16 5 C 4933 2.51 5 N 1182 2.21 5 O 1306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 7472 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1661 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Chain: "D" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1665 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "B" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1989 Classifications: {'peptide': 249} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 239} Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1989 Classifications: {'peptide': 249} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 239} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.11, per 1000 atoms: 0.28 Number of scatterers: 7472 At special positions: 0 Unit cell: (62.814, 104.139, 146.29, 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 51 16.00 O 1306 8.00 N 1182 7.00 C 4933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " 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: 0.63 Conformation dependent library (CDL) restraints added in 425.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 49.5% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.824A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.741A pdb=" N GLN C 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.752A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.895A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'B' and resid 25 through 49 removed outlier: 3.996A pdb=" N ARG B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 59 through 82 removed outlier: 3.673A pdb=" N GLY B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 78 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 117 removed outlier: 4.730A pdb=" N GLY B 97 " --> pdb=" O TYR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 153 removed outlier: 3.719A pdb=" N SER B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU B 139 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN B 140 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.541A pdb=" N MET B 161 " --> pdb=" O PHE B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'B' and resid 174 through 191 removed outlier: 3.608A pdb=" N THR B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 226 removed outlier: 3.562A pdb=" N GLY B 203 " --> pdb=" O TRP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 238 through 257 removed outlier: 3.508A pdb=" N TYR B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 268 removed outlier: 3.625A pdb=" N ARG B 267 " --> pdb=" O CYS B 263 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER B 268 " --> pdb=" O ILE B 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 46 removed outlier: 3.542A pdb=" N LEU A 26 " --> pdb=" O TRP A 22 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 50 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 59 through 82 removed outlier: 4.224A pdb=" N PHE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 119 removed outlier: 4.159A pdb=" N VAL A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLY A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 136 Processing helix chain 'A' and resid 137 through 154 Processing helix chain 'A' and resid 162 through 173 Processing helix chain 'A' and resid 174 through 190 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 199 through 226 removed outlier: 3.661A pdb=" N GLY A 203 " --> pdb=" O TRP A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 237 through 257 removed outlier: 3.656A pdb=" N TYR A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.835A pdb=" N THR C 33 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET C 34 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 57 " --> pdb=" O ASN C 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.139A pdb=" N TYR C 107 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 125 through 129 removed outlier: 4.727A pdb=" N ALA C 142 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 189 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLY C 144 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL C 187 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU C 146 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER C 185 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS C 148 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU C 183 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 125 through 129 removed outlier: 4.727A pdb=" N ALA C 142 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 189 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLY C 144 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL C 187 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU C 146 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER C 185 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS C 148 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU C 183 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 182 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 157 through 159 removed outlier: 3.791A pdb=" N LYS C 214 " --> pdb=" O CYS C 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.638A pdb=" N VAL D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.995A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 115 through 118 removed outlier: 3.767A pdb=" N ASN D 138 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 153 through 154 445 hydrogen bonds defined for protein. 1245 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: 1.22 Time building geometry restraints manager: 0.86 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: 2184 1.34 - 1.46: 1473 1.46 - 1.58: 3941 1.58 - 1.70: 0 1.70 - 1.81: 70 Bond restraints: 7668 Sorted by residual: bond pdb=" CA LYS C 219 " pdb=" CB LYS C 219 " ideal model delta sigma weight residual 1.513 1.550 -0.037 2.59e-02 1.49e+03 1.99e+00 bond pdb=" CA ILE B 24 " pdb=" CB ILE B 24 " ideal model delta sigma weight residual 1.540 1.559 -0.019 1.36e-02 5.41e+03 1.94e+00 bond pdb=" CB GLU D 187 " pdb=" CG GLU D 187 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.84e+00 bond pdb=" CA ILE B 24 " pdb=" C ILE B 24 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.27e-02 6.20e+03 1.72e+00 bond pdb=" C ALA B 89 " pdb=" N PRO B 90 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.28e-02 6.10e+03 1.61e+00 ... (remaining 7663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 10225 1.87 - 3.75: 207 3.75 - 5.62: 36 5.62 - 7.50: 16 7.50 - 9.37: 4 Bond angle restraints: 10488 Sorted by residual: angle pdb=" C GLY B 23 " pdb=" N ILE B 24 " pdb=" CA ILE B 24 " ideal model delta sigma weight residual 121.97 129.66 -7.69 1.80e+00 3.09e-01 1.82e+01 angle pdb=" CA GLN D 199 " pdb=" CB GLN D 199 " pdb=" CG GLN D 199 " ideal model delta sigma weight residual 114.10 120.78 -6.68 2.00e+00 2.50e-01 1.12e+01 angle pdb=" C MET A 157 " pdb=" N PHE A 158 " pdb=" CA PHE A 158 " ideal model delta sigma weight residual 121.54 127.60 -6.06 1.91e+00 2.74e-01 1.01e+01 angle pdb=" C VAL A 219 " pdb=" N TRP A 220 " pdb=" CA TRP A 220 " ideal model delta sigma weight residual 120.68 115.32 5.36 1.70e+00 3.46e-01 9.94e+00 angle pdb=" C ILE A 258 " pdb=" N VAL A 259 " pdb=" CA VAL A 259 " ideal model delta sigma weight residual 120.33 122.77 -2.44 8.00e-01 1.56e+00 9.33e+00 ... (remaining 10483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4425 17.90 - 35.79: 313 35.79 - 53.69: 42 53.69 - 71.59: 9 71.59 - 89.49: 7 Dihedral angle restraints: 4796 sinusoidal: 2074 harmonic: 2722 Sorted by residual: dihedral pdb=" CA ASN D 137 " pdb=" C ASN D 137 " pdb=" N ASN D 138 " pdb=" CA ASN D 138 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CB GLU C 138 " pdb=" CG GLU C 138 " pdb=" CD GLU C 138 " pdb=" OE1 GLU C 138 " ideal model delta sinusoidal sigma weight residual 0.00 89.49 -89.49 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA PHE A 158 " pdb=" C PHE A 158 " pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta harmonic sigma weight residual 180.00 -163.91 -16.09 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 4793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 791 0.035 - 0.070: 311 0.070 - 0.105: 114 0.105 - 0.139: 39 0.139 - 0.174: 3 Chirality restraints: 1258 Sorted by residual: chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA LEU B 60 " pdb=" N LEU B 60 " pdb=" C LEU B 60 " pdb=" CB LEU B 60 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE D 21 " pdb=" N ILE D 21 " pdb=" C ILE D 21 " pdb=" CB ILE D 21 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1255 not shown) Planarity restraints: 1251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 194 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO B 195 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 195 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 195 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 162 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO B 163 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 163 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 163 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 199 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C GLN D 199 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN D 199 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY D 200 " -0.009 2.00e-02 2.50e+03 ... (remaining 1248 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1957 2.81 - 3.33: 6779 3.33 - 3.86: 12273 3.86 - 4.38: 14656 4.38 - 4.90: 25006 Nonbonded interactions: 60671 Sorted by model distance: nonbonded pdb=" O LEU B 84 " pdb=" OG1 THR B 88 " model vdw 2.292 3.040 nonbonded pdb=" O GLN D 124 " pdb=" OG SER D 127 " model vdw 2.302 3.040 nonbonded pdb=" O CYS A 136 " pdb=" OH TYR A 176 " model vdw 2.311 3.040 nonbonded pdb=" O ASP D 82 " pdb=" OH TYR D 86 " model vdw 2.316 3.040 nonbonded pdb=" ND1 HIS A 202 " pdb=" OE2 GLU A 261 " model vdw 2.341 3.120 ... (remaining 60666 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 5.080 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.120 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7673 Z= 0.155 Angle : 0.697 9.374 10498 Z= 0.361 Chirality : 0.044 0.174 1258 Planarity : 0.006 0.052 1251 Dihedral : 12.294 89.486 3023 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 0.12 (0.27), residues: 925 helix: 0.75 (0.24), residues: 419 sheet: 0.60 (0.36), residues: 209 loop : -1.17 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 98 TYR 0.013 0.001 TYR D 140 PHE 0.019 0.002 PHE B 124 TRP 0.026 0.002 TRP B 220 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7668) covalent geometry : angle 0.69638 (10488) SS BOND : bond 0.00240 ( 5) SS BOND : angle 0.83037 ( 10) hydrogen bonds : bond 0.12185 ( 425) hydrogen bonds : angle 5.94321 ( 1245) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: C 43 GLN cc_start: 0.8773 (mm110) cc_final: 0.8464 (mm110) REVERT: C 46 GLU cc_start: 0.8689 (tt0) cc_final: 0.8261 (tt0) REVERT: C 214 LYS cc_start: 0.7651 (tppt) cc_final: 0.6677 (tppt) REVERT: D 3 GLN cc_start: 0.8349 (mm110) cc_final: 0.8117 (mp10) REVERT: D 42 LYS cc_start: 0.8378 (mppt) cc_final: 0.8057 (mmtp) REVERT: D 45 LYS cc_start: 0.8421 (mttt) cc_final: 0.8177 (mtpm) REVERT: D 93 ARG cc_start: 0.8009 (ptm-80) cc_final: 0.7708 (mtp85) REVERT: D 126 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7029 (pttp) REVERT: D 150 VAL cc_start: 0.7531 (t) cc_final: 0.7241 (p) REVERT: B 113 ASN cc_start: 0.8272 (t0) cc_final: 0.8042 (t160) REVERT: B 198 ASN cc_start: 0.8168 (t0) cc_final: 0.7808 (p0) REVERT: B 232 GLN cc_start: 0.7670 (mt0) cc_final: 0.7099 (mp-120) REVERT: A 50 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7636 (mptp) REVERT: A 116 LYS cc_start: 0.7939 (tttp) cc_final: 0.7649 (tttm) REVERT: A 233 ARG cc_start: 0.8008 (mmt90) cc_final: 0.7798 (mmt90) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.7207 time to fit residues: 101.2278 Evaluate side-chains 92 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.0170 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 249 ASN A 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.083394 restraints weight = 9005.057| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.99 r_work: 0.2807 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7673 Z= 0.196 Angle : 0.610 7.563 10498 Z= 0.310 Chirality : 0.044 0.160 1258 Planarity : 0.005 0.046 1251 Dihedral : 7.396 59.778 1387 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.70 % Allowed : 7.54 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 0.72 (0.28), residues: 925 helix: 1.38 (0.25), residues: 421 sheet: 0.62 (0.36), residues: 222 loop : -0.95 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 98 TYR 0.011 0.002 TYR C 150 PHE 0.018 0.002 PHE D 209 TRP 0.022 0.002 TRP B 237 HIS 0.005 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 7668) covalent geometry : angle 0.60867 (10488) SS BOND : bond 0.00531 ( 5) SS BOND : angle 1.49566 ( 10) hydrogen bonds : bond 0.04800 ( 425) hydrogen bonds : angle 4.44302 ( 1245) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.319 Fit side-chains REVERT: C 43 GLN cc_start: 0.8752 (mm110) cc_final: 0.8458 (mm110) REVERT: C 46 GLU cc_start: 0.8851 (tt0) cc_final: 0.8477 (tt0) REVERT: C 57 ASP cc_start: 0.8123 (t70) cc_final: 0.7834 (t0) REVERT: C 67 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.5646 (ptt90) REVERT: D 3 GLN cc_start: 0.8425 (mm110) cc_final: 0.8184 (mp-120) REVERT: D 45 LYS cc_start: 0.8622 (mttt) cc_final: 0.8360 (mtpm) REVERT: D 126 LYS cc_start: 0.7706 (mtmt) cc_final: 0.7080 (pttp) REVERT: D 179 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7035 (tp) REVERT: D 199 GLN cc_start: 0.8058 (pp30) cc_final: 0.7818 (pp30) REVERT: B 157 MET cc_start: 0.7135 (mtm) cc_final: 0.6820 (mtt) REVERT: B 198 ASN cc_start: 0.8300 (t0) cc_final: 0.7987 (p0) REVERT: B 232 GLN cc_start: 0.7560 (mt0) cc_final: 0.7000 (mp-120) REVERT: A 50 LYS cc_start: 0.8075 (mmtt) cc_final: 0.7870 (mptp) outliers start: 14 outliers final: 5 residues processed: 103 average time/residue: 0.7212 time to fit residues: 78.0017 Evaluate side-chains 92 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN D 155 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 86 GLN B 249 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.085027 restraints weight = 8946.117| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.99 r_work: 0.2832 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7673 Z= 0.123 Angle : 0.527 8.246 10498 Z= 0.268 Chirality : 0.041 0.139 1258 Planarity : 0.004 0.040 1251 Dihedral : 7.068 58.532 1387 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.95 % Allowed : 9.49 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 1.01 (0.28), residues: 925 helix: 1.74 (0.25), residues: 421 sheet: 0.66 (0.36), residues: 222 loop : -0.94 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.008 0.001 TYR D 91 PHE 0.015 0.001 PHE D 209 TRP 0.017 0.001 TRP B 220 HIS 0.005 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7668) covalent geometry : angle 0.52638 (10488) SS BOND : bond 0.00370 ( 5) SS BOND : angle 1.04007 ( 10) hydrogen bonds : bond 0.04061 ( 425) hydrogen bonds : angle 4.22522 ( 1245) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.302 Fit side-chains REVERT: C 43 GLN cc_start: 0.8751 (mm110) cc_final: 0.8452 (mm110) REVERT: C 46 GLU cc_start: 0.8841 (tt0) cc_final: 0.8491 (tt0) REVERT: C 57 ASP cc_start: 0.8131 (t70) cc_final: 0.7829 (t0) REVERT: C 67 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.5533 (ptt90) REVERT: D 3 GLN cc_start: 0.8400 (mm110) cc_final: 0.8159 (mp-120) REVERT: D 45 LYS cc_start: 0.8593 (mttt) cc_final: 0.8320 (mtpm) REVERT: D 126 LYS cc_start: 0.7756 (mtmt) cc_final: 0.7143 (pttp) REVERT: D 155 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7284 (mp10) REVERT: D 179 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7080 (tp) REVERT: B 157 MET cc_start: 0.7062 (mtm) cc_final: 0.6706 (mtt) REVERT: B 198 ASN cc_start: 0.8304 (t0) cc_final: 0.7971 (p0) REVERT: B 232 GLN cc_start: 0.7563 (mt0) cc_final: 0.7026 (mp-120) outliers start: 16 outliers final: 6 residues processed: 98 average time/residue: 0.7214 time to fit residues: 74.2153 Evaluate side-chains 89 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 241 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.078889 restraints weight = 9187.476| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.96 r_work: 0.2734 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 7673 Z= 0.353 Angle : 0.719 9.396 10498 Z= 0.362 Chirality : 0.050 0.176 1258 Planarity : 0.005 0.055 1251 Dihedral : 7.866 57.383 1387 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.31 % Allowed : 9.85 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 0.41 (0.28), residues: 925 helix: 1.20 (0.25), residues: 423 sheet: 0.51 (0.36), residues: 223 loop : -1.32 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 267 TYR 0.013 0.002 TYR C 95 PHE 0.024 0.002 PHE D 209 TRP 0.018 0.002 TRP B 237 HIS 0.003 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00879 ( 7668) covalent geometry : angle 0.71662 (10488) SS BOND : bond 0.00867 ( 5) SS BOND : angle 1.97152 ( 10) hydrogen bonds : bond 0.05784 ( 425) hydrogen bonds : angle 4.67260 ( 1245) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: C 43 GLN cc_start: 0.8767 (mm110) cc_final: 0.8448 (mm110) REVERT: C 46 GLU cc_start: 0.8827 (tt0) cc_final: 0.8538 (tt0) REVERT: C 57 ASP cc_start: 0.8112 (t70) cc_final: 0.7767 (t0) REVERT: C 67 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.5727 (ptt90) REVERT: D 3 GLN cc_start: 0.8468 (mm110) cc_final: 0.8241 (mp10) REVERT: D 45 LYS cc_start: 0.8640 (mttt) cc_final: 0.8357 (mtpm) REVERT: D 81 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7734 (pm20) REVERT: D 179 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.6961 (tp) REVERT: B 157 MET cc_start: 0.7388 (mtm) cc_final: 0.7049 (mtt) REVERT: A 86 GLN cc_start: 0.9406 (OUTLIER) cc_final: 0.9195 (mt0) outliers start: 19 outliers final: 9 residues processed: 99 average time/residue: 0.6800 time to fit residues: 70.8818 Evaluate side-chains 90 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 86 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN B 56 GLN B 86 GLN B 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.083501 restraints weight = 9042.458| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.99 r_work: 0.2805 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7673 Z= 0.119 Angle : 0.529 8.053 10498 Z= 0.271 Chirality : 0.041 0.142 1258 Planarity : 0.004 0.041 1251 Dihedral : 7.180 59.709 1387 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.82 % Allowed : 11.56 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 0.89 (0.28), residues: 925 helix: 1.73 (0.25), residues: 423 sheet: 0.58 (0.35), residues: 224 loop : -1.16 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 93 TYR 0.008 0.001 TYR D 91 PHE 0.013 0.001 PHE D 209 TRP 0.019 0.001 TRP B 220 HIS 0.004 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7668) covalent geometry : angle 0.52807 (10488) SS BOND : bond 0.00329 ( 5) SS BOND : angle 0.92191 ( 10) hydrogen bonds : bond 0.04091 ( 425) hydrogen bonds : angle 4.28333 ( 1245) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.313 Fit side-chains REVERT: C 43 GLN cc_start: 0.8715 (mm110) cc_final: 0.8448 (mm110) REVERT: C 46 GLU cc_start: 0.8826 (tt0) cc_final: 0.8452 (tt0) REVERT: C 57 ASP cc_start: 0.8149 (t70) cc_final: 0.7822 (t0) REVERT: C 67 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.5507 (ptt90) REVERT: D 3 GLN cc_start: 0.8486 (mm110) cc_final: 0.8148 (mp-120) REVERT: D 45 LYS cc_start: 0.8529 (mttt) cc_final: 0.8249 (mtpm) REVERT: D 179 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7064 (tp) REVERT: B 157 MET cc_start: 0.7181 (mtm) cc_final: 0.6780 (mtt) outliers start: 15 outliers final: 6 residues processed: 95 average time/residue: 0.6699 time to fit residues: 66.9969 Evaluate side-chains 84 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 241 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.0170 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 249 ASN A 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.083224 restraints weight = 8972.257| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.99 r_work: 0.2803 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7673 Z= 0.136 Angle : 0.535 7.895 10498 Z= 0.273 Chirality : 0.041 0.159 1258 Planarity : 0.004 0.041 1251 Dihedral : 7.176 59.881 1387 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.57 % Rotamer: Outliers : 1.95 % Allowed : 11.68 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 1.02 (0.28), residues: 925 helix: 1.86 (0.25), residues: 423 sheet: 0.56 (0.35), residues: 224 loop : -1.07 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 93 TYR 0.009 0.001 TYR D 91 PHE 0.021 0.001 PHE D 209 TRP 0.018 0.001 TRP B 220 HIS 0.001 0.000 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 7668) covalent geometry : angle 0.53452 (10488) SS BOND : bond 0.00382 ( 5) SS BOND : angle 1.06943 ( 10) hydrogen bonds : bond 0.04111 ( 425) hydrogen bonds : angle 4.22294 ( 1245) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: C 43 GLN cc_start: 0.8719 (mm110) cc_final: 0.8423 (mm110) REVERT: C 46 GLU cc_start: 0.8818 (tt0) cc_final: 0.8440 (tt0) REVERT: C 57 ASP cc_start: 0.8156 (t70) cc_final: 0.7828 (t0) REVERT: C 67 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.5421 (ptt90) REVERT: D 45 LYS cc_start: 0.8564 (mttt) cc_final: 0.8272 (mtpm) REVERT: D 179 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7070 (tp) REVERT: B 157 MET cc_start: 0.7088 (mtm) cc_final: 0.6729 (mtt) outliers start: 16 outliers final: 11 residues processed: 91 average time/residue: 0.6338 time to fit residues: 60.7556 Evaluate side-chains 90 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 156 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 84 optimal weight: 0.0370 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 249 ASN A 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.085385 restraints weight = 8990.293| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.00 r_work: 0.2840 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7673 Z= 0.103 Angle : 0.502 8.031 10498 Z= 0.257 Chirality : 0.040 0.159 1258 Planarity : 0.004 0.040 1251 Dihedral : 6.951 59.924 1387 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.22 % Favored : 95.68 % Rotamer: Outliers : 1.95 % Allowed : 11.80 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 1.23 (0.28), residues: 925 helix: 2.07 (0.25), residues: 423 sheet: 0.60 (0.35), residues: 224 loop : -0.97 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 93 TYR 0.007 0.001 TYR D 91 PHE 0.016 0.001 PHE D 209 TRP 0.018 0.001 TRP B 220 HIS 0.003 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7668) covalent geometry : angle 0.50170 (10488) SS BOND : bond 0.00283 ( 5) SS BOND : angle 0.91010 ( 10) hydrogen bonds : bond 0.03679 ( 425) hydrogen bonds : angle 4.07571 ( 1245) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 GLN cc_start: 0.8736 (mm110) cc_final: 0.8483 (mm110) REVERT: C 46 GLU cc_start: 0.8820 (tt0) cc_final: 0.8448 (tt0) REVERT: C 57 ASP cc_start: 0.8137 (t70) cc_final: 0.7823 (t0) REVERT: C 67 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.5518 (ptt90) REVERT: D 45 LYS cc_start: 0.8573 (mttt) cc_final: 0.8293 (mtpm) REVERT: D 179 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7124 (tp) REVERT: B 157 MET cc_start: 0.7061 (mtm) cc_final: 0.6708 (mtt) outliers start: 16 outliers final: 8 residues processed: 93 average time/residue: 0.6786 time to fit residues: 66.4207 Evaluate side-chains 86 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 156 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 67 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 249 ASN A 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.083817 restraints weight = 9026.628| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.06 r_work: 0.2791 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7673 Z= 0.150 Angle : 0.543 7.922 10498 Z= 0.276 Chirality : 0.042 0.180 1258 Planarity : 0.004 0.042 1251 Dihedral : 7.147 59.161 1387 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 2.07 % Allowed : 11.80 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 1.18 (0.28), residues: 925 helix: 1.99 (0.25), residues: 423 sheet: 0.67 (0.36), residues: 222 loop : -1.00 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 93 TYR 0.010 0.001 TYR D 91 PHE 0.033 0.002 PHE D 209 TRP 0.016 0.001 TRP B 220 HIS 0.003 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7668) covalent geometry : angle 0.54181 (10488) SS BOND : bond 0.00438 ( 5) SS BOND : angle 1.18719 ( 10) hydrogen bonds : bond 0.04150 ( 425) hydrogen bonds : angle 4.14778 ( 1245) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: C 43 GLN cc_start: 0.8748 (mm110) cc_final: 0.8456 (mm110) REVERT: C 46 GLU cc_start: 0.8856 (tt0) cc_final: 0.8483 (tt0) REVERT: C 57 ASP cc_start: 0.8174 (t70) cc_final: 0.7847 (t0) REVERT: C 67 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.5689 (ptt90) REVERT: D 45 LYS cc_start: 0.8616 (mttt) cc_final: 0.8336 (mtpm) REVERT: D 179 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7055 (tp) REVERT: B 157 MET cc_start: 0.7110 (mtm) cc_final: 0.6734 (mtt) outliers start: 17 outliers final: 10 residues processed: 92 average time/residue: 0.6977 time to fit residues: 67.5216 Evaluate side-chains 88 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 59 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 249 ASN A 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.084144 restraints weight = 8939.986| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.97 r_work: 0.2817 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7673 Z= 0.127 Angle : 0.523 7.928 10498 Z= 0.267 Chirality : 0.041 0.183 1258 Planarity : 0.004 0.040 1251 Dihedral : 7.068 59.466 1387 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 1.95 % Allowed : 12.17 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 1.24 (0.28), residues: 925 helix: 2.05 (0.25), residues: 423 sheet: 0.66 (0.36), residues: 222 loop : -0.96 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 93 TYR 0.009 0.001 TYR D 91 PHE 0.030 0.001 PHE D 209 TRP 0.017 0.001 TRP B 220 HIS 0.004 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7668) covalent geometry : angle 0.52261 (10488) SS BOND : bond 0.00375 ( 5) SS BOND : angle 1.10404 ( 10) hydrogen bonds : bond 0.03949 ( 425) hydrogen bonds : angle 4.10329 ( 1245) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: C 43 GLN cc_start: 0.8725 (mm110) cc_final: 0.8429 (mm110) REVERT: C 46 GLU cc_start: 0.8806 (tt0) cc_final: 0.8422 (tt0) REVERT: C 57 ASP cc_start: 0.8159 (t70) cc_final: 0.7832 (t0) REVERT: C 67 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.5429 (ptt90) REVERT: D 45 LYS cc_start: 0.8580 (mttt) cc_final: 0.8294 (mtpm) REVERT: D 150 VAL cc_start: 0.7419 (t) cc_final: 0.7209 (p) REVERT: D 179 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.6953 (tp) REVERT: B 157 MET cc_start: 0.7061 (mtm) cc_final: 0.6701 (mtt) outliers start: 16 outliers final: 11 residues processed: 92 average time/residue: 0.6552 time to fit residues: 63.4916 Evaluate side-chains 90 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 156 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 70 optimal weight: 0.3980 chunk 22 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 0.0770 chunk 90 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN A 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.122602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.085113 restraints weight = 8929.246| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.98 r_work: 0.2832 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 0.029 7673 Z= 0.112 Angle : 0.516 7.997 10498 Z= 0.262 Chirality : 0.041 0.177 1258 Planarity : 0.004 0.041 1251 Dihedral : 6.972 59.910 1387 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.65 % Favored : 95.24 % Rotamer: Outliers : 1.58 % Allowed : 12.65 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 1.30 (0.29), residues: 925 helix: 2.13 (0.25), residues: 423 sheet: 0.63 (0.35), residues: 224 loop : -0.92 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 93 TYR 0.008 0.001 TYR D 91 PHE 0.027 0.001 PHE D 209 TRP 0.018 0.001 TRP B 220 HIS 0.004 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7668) covalent geometry : angle 0.51548 (10488) SS BOND : bond 0.00325 ( 5) SS BOND : angle 1.02275 ( 10) hydrogen bonds : bond 0.03754 ( 425) hydrogen bonds : angle 4.03135 ( 1245) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: C 43 GLN cc_start: 0.8714 (mm110) cc_final: 0.8423 (mm110) REVERT: C 46 GLU cc_start: 0.8749 (tt0) cc_final: 0.8400 (tt0) REVERT: C 57 ASP cc_start: 0.8138 (t70) cc_final: 0.7817 (t0) REVERT: C 67 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.5449 (ptt90) REVERT: D 45 LYS cc_start: 0.8567 (mttt) cc_final: 0.8285 (mtpm) REVERT: D 150 VAL cc_start: 0.7405 (t) cc_final: 0.7150 (p) REVERT: D 179 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.6953 (tp) REVERT: B 157 MET cc_start: 0.7037 (mtm) cc_final: 0.6711 (mtt) outliers start: 13 outliers final: 8 residues processed: 87 average time/residue: 0.6828 time to fit residues: 62.5577 Evaluate side-chains 86 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 11 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN A 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.082590 restraints weight = 8988.657| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.97 r_work: 0.2798 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7673 Z= 0.171 Angle : 0.569 7.871 10498 Z= 0.287 Chirality : 0.043 0.169 1258 Planarity : 0.004 0.042 1251 Dihedral : 7.234 58.235 1387 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.57 % Rotamer: Outliers : 1.70 % Allowed : 12.17 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.50 % 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: 1.12 (0.28), residues: 925 helix: 1.95 (0.25), residues: 423 sheet: 0.62 (0.36), residues: 222 loop : -1.04 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 93 TYR 0.010 0.002 TYR D 91 PHE 0.028 0.002 PHE D 209 TRP 0.016 0.001 TRP A 220 HIS 0.004 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 7668) covalent geometry : angle 0.56771 (10488) SS BOND : bond 0.00500 ( 5) SS BOND : angle 1.40995 ( 10) hydrogen bonds : bond 0.04370 ( 425) hydrogen bonds : angle 4.19577 ( 1245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3198.56 seconds wall clock time: 55 minutes 20.22 seconds (3320.22 seconds total)