Starting phenix.real_space_refine on Fri Dec 27 18:39:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fja_29220/12_2024/8fja_29220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fja_29220/12_2024/8fja_29220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fja_29220/12_2024/8fja_29220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fja_29220/12_2024/8fja_29220.map" model { file = "/net/cci-nas-00/data/ceres_data/8fja_29220/12_2024/8fja_29220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fja_29220/12_2024/8fja_29220.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 27 5.16 5 C 4024 2.51 5 N 1117 2.21 5 O 1251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6419 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 1645 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 214, 1645 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 203} Chain: "E" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1620 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Chain: "A" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2237 Classifications: {'peptide': 274} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 262} Chain: "B" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 837 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 80 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Time building chain proxies: 4.55, per 1000 atoms: 0.71 Number of scatterers: 6419 At special positions: 0 Unit cell: (138.55, 103.7, 68.85, 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 27 16.00 O 1251 8.00 N 1117 7.00 C 4024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS E 135 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 148 " - pdb=" SG CYS E 204 " distance=2.04 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 957.7 milliseconds 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1510 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 19 sheets defined 13.2% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'D' and resid 121 through 125 removed outlier: 3.618A pdb=" N LEU D 125 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.861A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.074A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 197 removed outlier: 3.703A pdb=" N LEU E 197 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.545A pdb=" N ILE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU A 53 " --> pdb=" O PRO A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 53' Processing helix chain 'A' and resid 56 through 85 removed outlier: 3.620A pdb=" N TRP A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 removed outlier: 4.173A pdb=" N THR A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 161 removed outlier: 4.045A pdb=" N GLN A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 252 through 255 removed outlier: 4.498A pdb=" N GLN A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.937A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 67 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.512A pdb=" N ALA D 13 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.735A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 114 through 115 removed outlier: 4.281A pdb=" N SER D 114 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN D 137 " --> pdb=" O SER D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 145 through 149 removed outlier: 4.351A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR D 197 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS D 149 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA D 193 " --> pdb=" O LYS D 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA7, first strand: chain 'D' and resid 163 through 164 removed outlier: 4.076A pdb=" N SER D 174 " --> pdb=" O THR D 164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.871A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.530A pdb=" N VAL E 110 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 131 removed outlier: 3.521A pdb=" N SER E 128 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA E 145 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL E 192 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY E 147 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL E 190 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU E 149 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N SER E 188 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS E 151 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU E 186 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR E 153 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N SER E 187 " --> pdb=" O PRO E 175 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL E 189 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR E 173 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 161 through 162 removed outlier: 4.269A pdb=" N CYS E 204 " --> pdb=" O LYS E 217 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS E 217 " --> pdb=" O CYS E 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.861A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG A 35 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA A 24 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASP A 37 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE A 22 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 111 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N HIS A 114 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 124 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TYR A 118 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 186 through 193 removed outlier: 3.573A pdb=" N HIS A 188 " --> pdb=" O TRP A 204 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 186 through 193 removed outlier: 3.573A pdb=" N HIS A 188 " --> pdb=" O TRP A 204 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 222 through 223 removed outlier: 3.536A pdb=" N VAL A 261 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.772A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.772A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 44 through 45 259 hydrogen bonds defined for protein. 660 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: 1.83 Time building geometry restraints manager: 1.76 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: 2110 1.34 - 1.46: 1654 1.46 - 1.58: 2778 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 6580 Sorted by residual: bond pdb=" CG ARG A 6 " pdb=" CD ARG A 6 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 2.00e+00 bond pdb=" CB PRO B 32 " pdb=" CG PRO B 32 " ideal model delta sigma weight residual 1.506 1.453 0.053 3.90e-02 6.57e+02 1.82e+00 bond pdb=" SD MET E 108 " pdb=" CE MET E 108 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.79e+00 bond pdb=" CD LYS B 19 " pdb=" CE LYS B 19 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CB PRO A 210 " pdb=" CG PRO A 210 " ideal model delta sigma weight residual 1.506 1.457 0.049 3.90e-02 6.57e+02 1.56e+00 ... (remaining 6575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 8557 1.78 - 3.56: 308 3.56 - 5.34: 47 5.34 - 7.13: 12 7.13 - 8.91: 9 Bond angle restraints: 8933 Sorted by residual: angle pdb=" CA ARG E 218 " pdb=" CB ARG E 218 " pdb=" CG ARG E 218 " ideal model delta sigma weight residual 114.10 122.84 -8.74 2.00e+00 2.50e-01 1.91e+01 angle pdb=" N ARG A 17 " pdb=" CA ARG A 17 " pdb=" C ARG A 17 " ideal model delta sigma weight residual 107.49 116.40 -8.91 2.16e+00 2.14e-01 1.70e+01 angle pdb=" C GLU B 16 " pdb=" CA GLU B 16 " pdb=" CB GLU B 16 " ideal model delta sigma weight residual 109.70 117.03 -7.33 1.81e+00 3.05e-01 1.64e+01 angle pdb=" C LYS B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta sigma weight residual 121.81 129.99 -8.18 2.16e+00 2.14e-01 1.43e+01 angle pdb=" N ASN B 17 " pdb=" CA ASN B 17 " pdb=" C ASN B 17 " ideal model delta sigma weight residual 110.10 115.20 -5.10 1.49e+00 4.50e-01 1.17e+01 ... (remaining 8928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 3561 16.59 - 33.19: 283 33.19 - 49.78: 45 49.78 - 66.38: 11 66.38 - 82.97: 8 Dihedral angle restraints: 3908 sinusoidal: 1554 harmonic: 2354 Sorted by residual: dihedral pdb=" CB CYS E 148 " pdb=" SG CYS E 148 " pdb=" SG CYS E 204 " pdb=" CB CYS E 204 " ideal model delta sinusoidal sigma weight residual 93.00 143.03 -50.03 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual 93.00 52.16 40.84 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CB CYS B 25 " pdb=" SG CYS B 25 " pdb=" SG CYS B 80 " pdb=" CB CYS B 80 " ideal model delta sinusoidal sigma weight residual -86.00 -113.49 27.49 1 1.00e+01 1.00e-02 1.08e+01 ... (remaining 3905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 587 0.040 - 0.080: 266 0.080 - 0.119: 68 0.119 - 0.159: 29 0.159 - 0.199: 7 Chirality restraints: 957 Sorted by residual: chirality pdb=" CA LYS B 19 " pdb=" N LYS B 19 " pdb=" C LYS B 19 " pdb=" CB LYS B 19 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CB THR E 173 " pdb=" CA THR E 173 " pdb=" OG1 THR E 173 " pdb=" CG2 THR E 173 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" CB ILE D 106 " pdb=" CA ILE D 106 " pdb=" CG1 ILE D 106 " pdb=" CG2 ILE D 106 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 954 not shown) Planarity restraints: 1157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 174 " -0.064 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO E 175 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 175 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 175 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 79 " 0.061 5.00e-02 4.00e+02 9.21e-02 1.36e+01 pdb=" N PRO D 80 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 19 " 0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO A 20 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 20 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 20 " 0.037 5.00e-02 4.00e+02 ... (remaining 1154 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 914 2.76 - 3.29: 5434 3.29 - 3.83: 9750 3.83 - 4.36: 12022 4.36 - 4.90: 21803 Nonbonded interactions: 49923 Sorted by model distance: nonbonded pdb=" O GLN A 255 " pdb=" NH2 ARG A 273 " model vdw 2.220 3.120 nonbonded pdb=" NE2 GLN D 147 " pdb=" O GLN D 155 " model vdw 2.288 3.120 nonbonded pdb=" OD2 ASP A 220 " pdb=" NH1 ARG A 256 " model vdw 2.295 3.120 nonbonded pdb=" O SER E 196 " pdb=" OG SER E 196 " model vdw 2.321 3.040 nonbonded pdb=" O GLN D 124 " pdb=" OG SER D 127 " model vdw 2.331 3.040 ... (remaining 49918 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: 1.860 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.700 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.007 0.053 6580 Z= 0.453 Angle : 0.818 8.907 8933 Z= 0.432 Chirality : 0.051 0.199 957 Planarity : 0.006 0.096 1157 Dihedral : 12.620 82.970 2374 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.27), residues: 800 helix: -1.37 (0.52), residues: 79 sheet: -1.37 (0.27), residues: 333 loop : -2.06 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 100 HIS 0.007 0.001 HIS E 208 PHE 0.031 0.002 PHE B 70 TYR 0.025 0.002 TYR A 113 ARG 0.014 0.001 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: E 73 ASP cc_start: 0.8497 (t70) cc_final: 0.8252 (t70) REVERT: E 108 MET cc_start: 0.8701 (mpp) cc_final: 0.8219 (mpt) REVERT: A 173 GLU cc_start: 0.8080 (tp30) cc_final: 0.7730 (tp30) REVERT: A 219 ARG cc_start: 0.8711 (ttp80) cc_final: 0.8290 (ttt-90) REVERT: A 255 GLN cc_start: 0.9172 (mm110) cc_final: 0.8836 (mm110) REVERT: B 76 ASP cc_start: 0.8614 (m-30) cc_final: 0.8387 (m-30) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 1.7523 time to fit residues: 150.9135 Evaluate side-chains 76 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN A 224 GLN B 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6580 Z= 0.241 Angle : 0.604 6.657 8933 Z= 0.321 Chirality : 0.044 0.148 957 Planarity : 0.005 0.069 1157 Dihedral : 4.740 21.889 890 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.00 % Allowed : 7.40 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.29), residues: 800 helix: -0.39 (0.57), residues: 78 sheet: -0.68 (0.28), residues: 339 loop : -1.47 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 100 HIS 0.004 0.001 HIS E 208 PHE 0.014 0.001 PHE B 70 TYR 0.014 0.001 TYR A 99 ARG 0.004 0.001 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.732 Fit side-chains REVERT: A 58 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: A 121 LYS cc_start: 0.8970 (ptpp) cc_final: 0.8621 (ptpp) REVERT: A 173 GLU cc_start: 0.8151 (tp30) cc_final: 0.7805 (tp30) REVERT: A 255 GLN cc_start: 0.9215 (mm110) cc_final: 0.8823 (mm110) outliers start: 7 outliers final: 1 residues processed: 72 average time/residue: 1.8609 time to fit residues: 138.9393 Evaluate side-chains 67 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6580 Z= 0.237 Angle : 0.561 6.044 8933 Z= 0.298 Chirality : 0.043 0.148 957 Planarity : 0.005 0.069 1157 Dihedral : 4.575 22.209 890 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.14 % Allowed : 9.96 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.29), residues: 800 helix: -0.29 (0.57), residues: 84 sheet: -0.25 (0.28), residues: 335 loop : -1.29 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 100 HIS 0.003 0.001 HIS E 95 PHE 0.012 0.001 PHE B 70 TYR 0.014 0.001 TYR A 113 ARG 0.004 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.762 Fit side-chains REVERT: A 58 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: A 121 LYS cc_start: 0.8942 (ptpp) cc_final: 0.8627 (ptpp) REVERT: A 173 GLU cc_start: 0.8180 (tp30) cc_final: 0.7794 (tp30) REVERT: A 219 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8181 (ttt-90) REVERT: A 255 GLN cc_start: 0.9202 (mm110) cc_final: 0.8800 (mm110) REVERT: B 44 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7776 (mt-10) outliers start: 8 outliers final: 2 residues processed: 70 average time/residue: 1.7749 time to fit residues: 128.9758 Evaluate side-chains 65 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 44 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 30.0000 chunk 64 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6580 Z= 0.284 Angle : 0.561 5.848 8933 Z= 0.298 Chirality : 0.043 0.156 957 Planarity : 0.005 0.063 1157 Dihedral : 4.587 25.629 890 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.71 % Allowed : 11.81 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.29), residues: 800 helix: -0.27 (0.57), residues: 84 sheet: -0.05 (0.28), residues: 335 loop : -1.22 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 100 HIS 0.004 0.001 HIS E 95 PHE 0.013 0.002 PHE A 208 TYR 0.013 0.001 TYR B 63 ARG 0.004 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.719 Fit side-chains REVERT: E 125 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7357 (tmtp) REVERT: E 183 LEU cc_start: 0.8545 (mm) cc_final: 0.8283 (mm) REVERT: A 58 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: A 121 LYS cc_start: 0.8950 (ptpp) cc_final: 0.8607 (ptpp) REVERT: A 173 GLU cc_start: 0.8199 (tp30) cc_final: 0.7828 (tp30) REVERT: A 219 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8278 (ttt-90) REVERT: A 255 GLN cc_start: 0.9203 (mm110) cc_final: 0.8831 (mm110) REVERT: B 76 ASP cc_start: 0.8614 (m-30) cc_final: 0.8397 (m-30) REVERT: B 96 ASP cc_start: 0.8239 (t0) cc_final: 0.7817 (t0) outliers start: 12 outliers final: 4 residues processed: 70 average time/residue: 1.7490 time to fit residues: 127.2901 Evaluate side-chains 67 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6580 Z= 0.334 Angle : 0.565 5.284 8933 Z= 0.301 Chirality : 0.044 0.164 957 Planarity : 0.005 0.059 1157 Dihedral : 4.651 27.976 890 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.85 % Allowed : 12.09 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.29), residues: 800 helix: -0.29 (0.56), residues: 84 sheet: 0.05 (0.28), residues: 345 loop : -1.13 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 100 HIS 0.004 0.001 HIS E 95 PHE 0.013 0.002 PHE A 208 TYR 0.014 0.001 TYR B 63 ARG 0.003 0.001 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.732 Fit side-chains REVERT: E 183 LEU cc_start: 0.8559 (mm) cc_final: 0.8302 (mm) REVERT: A 58 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: A 121 LYS cc_start: 0.9006 (ptpp) cc_final: 0.8721 (ptpp) REVERT: A 255 GLN cc_start: 0.9215 (mm110) cc_final: 0.8891 (mm110) REVERT: B 44 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: B 94 LYS cc_start: 0.8996 (mttt) cc_final: 0.8725 (mttm) REVERT: B 96 ASP cc_start: 0.8304 (t0) cc_final: 0.7992 (t0) outliers start: 13 outliers final: 6 residues processed: 67 average time/residue: 2.0478 time to fit residues: 142.6579 Evaluate side-chains 65 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 30.0000 chunk 77 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 chunk 40 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6580 Z= 0.191 Angle : 0.500 4.900 8933 Z= 0.267 Chirality : 0.042 0.140 957 Planarity : 0.004 0.054 1157 Dihedral : 4.364 25.264 890 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.42 % Allowed : 12.94 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.30), residues: 800 helix: 0.02 (0.58), residues: 84 sheet: 0.26 (0.29), residues: 332 loop : -1.03 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 100 HIS 0.003 0.001 HIS E 95 PHE 0.009 0.001 PHE D 91 TYR 0.011 0.001 TYR A 99 ARG 0.004 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.741 Fit side-chains REVERT: D 165 GLU cc_start: 0.7634 (pm20) cc_final: 0.7198 (pp20) REVERT: E 104 ASN cc_start: 0.8778 (m110) cc_final: 0.8409 (m110) REVERT: E 125 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7444 (tmtp) REVERT: E 183 LEU cc_start: 0.8562 (mm) cc_final: 0.8292 (mm) REVERT: A 58 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: A 121 LYS cc_start: 0.8897 (ptpp) cc_final: 0.8639 (ptpp) REVERT: A 255 GLN cc_start: 0.9216 (mm110) cc_final: 0.8894 (mm110) REVERT: B 74 GLU cc_start: 0.7754 (mp0) cc_final: 0.7547 (mp0) REVERT: B 94 LYS cc_start: 0.8998 (mttt) cc_final: 0.8646 (mttm) outliers start: 10 outliers final: 6 residues processed: 67 average time/residue: 1.7650 time to fit residues: 123.4248 Evaluate side-chains 64 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6580 Z= 0.213 Angle : 0.515 5.266 8933 Z= 0.274 Chirality : 0.042 0.143 957 Planarity : 0.004 0.052 1157 Dihedral : 4.310 24.717 890 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.28 % Allowed : 13.66 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.30), residues: 800 helix: 0.06 (0.57), residues: 84 sheet: 0.35 (0.29), residues: 332 loop : -0.96 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 100 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE D 91 TYR 0.013 0.001 TYR A 113 ARG 0.004 0.000 ARG E 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.711 Fit side-chains REVERT: D 165 GLU cc_start: 0.7701 (pm20) cc_final: 0.7207 (pp20) REVERT: E 125 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7548 (tmtp) REVERT: E 183 LEU cc_start: 0.8522 (mm) cc_final: 0.8292 (mm) REVERT: A 58 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: A 121 LYS cc_start: 0.8938 (ptpp) cc_final: 0.8517 (ptpp) REVERT: B 94 LYS cc_start: 0.9001 (mttt) cc_final: 0.8657 (mttm) REVERT: B 99 MET cc_start: 0.7629 (ttm) cc_final: 0.7345 (ttp) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 1.6369 time to fit residues: 107.5664 Evaluate side-chains 64 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 0.0970 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6580 Z= 0.188 Angle : 0.509 5.124 8933 Z= 0.271 Chirality : 0.041 0.140 957 Planarity : 0.004 0.051 1157 Dihedral : 4.218 23.536 890 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.28 % Allowed : 13.94 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.30), residues: 800 helix: 0.60 (0.60), residues: 78 sheet: 0.39 (0.29), residues: 332 loop : -0.83 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 100 HIS 0.003 0.001 HIS E 35 PHE 0.009 0.001 PHE D 91 TYR 0.010 0.001 TYR A 99 ARG 0.005 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.722 Fit side-chains REVERT: D 165 GLU cc_start: 0.7683 (pm20) cc_final: 0.7192 (pp20) REVERT: E 104 ASN cc_start: 0.8779 (m110) cc_final: 0.8431 (m110) REVERT: E 125 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7531 (tmtp) REVERT: E 183 LEU cc_start: 0.8537 (mm) cc_final: 0.8318 (mm) REVERT: A 58 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: A 121 LYS cc_start: 0.8911 (ptpp) cc_final: 0.8652 (ptpp) REVERT: A 253 GLN cc_start: 0.8878 (mt0) cc_final: 0.8528 (mt0) REVERT: B 94 LYS cc_start: 0.9003 (mttt) cc_final: 0.8664 (mttm) outliers start: 9 outliers final: 6 residues processed: 63 average time/residue: 1.6396 time to fit residues: 107.8920 Evaluate side-chains 63 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 46 optimal weight: 0.0040 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6580 Z= 0.154 Angle : 0.488 4.968 8933 Z= 0.260 Chirality : 0.041 0.140 957 Planarity : 0.004 0.052 1157 Dihedral : 4.039 17.815 890 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.14 % Allowed : 13.80 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.30), residues: 800 helix: 0.75 (0.61), residues: 78 sheet: 0.43 (0.29), residues: 332 loop : -0.73 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 100 HIS 0.003 0.001 HIS E 35 PHE 0.008 0.001 PHE D 91 TYR 0.010 0.001 TYR A 113 ARG 0.003 0.000 ARG E 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: D 40 ARG cc_start: 0.8501 (tpp-160) cc_final: 0.8128 (ttp-110) REVERT: E 104 ASN cc_start: 0.8781 (m110) cc_final: 0.8449 (m110) REVERT: E 125 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7541 (tmtp) REVERT: E 183 LEU cc_start: 0.8545 (mm) cc_final: 0.8330 (mm) REVERT: A 58 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: A 121 LYS cc_start: 0.8866 (ptpp) cc_final: 0.8612 (ptpp) REVERT: B 94 LYS cc_start: 0.9006 (mttt) cc_final: 0.8674 (mttm) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 1.7010 time to fit residues: 109.8720 Evaluate side-chains 63 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 6580 Z= 0.290 Angle : 0.547 5.729 8933 Z= 0.290 Chirality : 0.043 0.156 957 Planarity : 0.004 0.050 1157 Dihedral : 4.231 18.139 890 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.14 % Allowed : 14.51 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.30), residues: 800 helix: 0.47 (0.60), residues: 78 sheet: 0.41 (0.29), residues: 325 loop : -0.74 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 100 HIS 0.004 0.001 HIS E 95 PHE 0.013 0.002 PHE D 91 TYR 0.013 0.001 TYR B 63 ARG 0.005 0.000 ARG E 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: D 40 ARG cc_start: 0.8524 (tpp-160) cc_final: 0.8173 (ttp-110) REVERT: E 125 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7623 (tmtp) REVERT: E 183 LEU cc_start: 0.8516 (mm) cc_final: 0.8285 (mm) REVERT: A 58 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: A 121 LYS cc_start: 0.8953 (ptpp) cc_final: 0.8660 (ptpp) REVERT: B 94 LYS cc_start: 0.9018 (mttt) cc_final: 0.8677 (mttm) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 1.9911 time to fit residues: 128.5567 Evaluate side-chains 65 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 HIS ** 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 = 0.3841 r_free = 0.3841 target = 0.140639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.077558 restraints weight = 8482.771| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.65 r_work: 0.2711 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6580 Z= 0.188 Angle : 0.503 4.893 8933 Z= 0.268 Chirality : 0.041 0.141 957 Planarity : 0.004 0.051 1157 Dihedral : 4.143 18.165 890 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.14 % Allowed : 14.65 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.30), residues: 800 helix: 0.67 (0.60), residues: 78 sheet: 0.45 (0.29), residues: 325 loop : -0.66 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 100 HIS 0.003 0.001 HIS E 35 PHE 0.009 0.001 PHE D 91 TYR 0.010 0.001 TYR A 99 ARG 0.005 0.000 ARG E 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2831.20 seconds wall clock time: 52 minutes 2.00 seconds (3122.00 seconds total)