Starting phenix.real_space_refine on Tue Mar 11 16:08:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iec_35378/03_2025/8iec_35378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iec_35378/03_2025/8iec_35378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iec_35378/03_2025/8iec_35378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iec_35378/03_2025/8iec_35378.map" model { file = "/net/cci-nas-00/data/ceres_data/8iec_35378/03_2025/8iec_35378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iec_35378/03_2025/8iec_35378.cif" } resolution = 3.18 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= 0.014 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 44 5.16 5 C 3954 2.51 5 N 1079 2.21 5 O 1201 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6278 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1659 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2527 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "N" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1707 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "Y" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 385 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 4.90, per 1000 atoms: 0.78 Number of scatterers: 6278 At special positions: 0 Unit cell: (89.1, 119.88, 82.62, 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 44 16.00 O 1201 8.00 N 1079 7.00 C 3954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 147 " - pdb=" SG CYS N 217 " 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: 1.43 Conformation dependent library (CDL) restraints added in 893.1 milliseconds 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1554 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 13 sheets defined 19.1% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 96 through 102 removed outlier: 3.563A pdb=" N GLU C 101 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP C 102 " --> pdb=" O CYS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 130 through 135 removed outlier: 6.292A pdb=" N PHE C 133 " --> pdb=" O ASN C 130 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C 135 " --> pdb=" O LYS C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 153 Processing helix chain 'C' and resid 170 through 184 Processing helix chain 'C' and resid 205 through 225 Processing helix chain 'D' and resid 4 through 25 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.581A pdb=" N SER N 31 " --> pdb=" O ALA N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.722A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.699A pdb=" N ASP N 90 " --> pdb=" O THR N 87 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 87 through 91' Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.504A pdb=" N MET Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU Y 22 " --> pdb=" O GLN Y 18 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 34 through 44 removed outlier: 3.592A pdb=" N MET Y 38 " --> pdb=" O ALA Y 34 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU Y 42 " --> pdb=" O MET Y 38 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.987A pdb=" N ALA C 105 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE C 139 " --> pdb=" O TYR C 194 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N HIS C 196 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU C 141 " --> pdb=" O HIS C 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.750A pdb=" N VAL D 327 " --> pdb=" O TRP D 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.561A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA D 73 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.988A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY D 116 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 151 removed outlier: 6.648A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE D 151 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLN D 156 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS D 166 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 191 through 192 removed outlier: 4.021A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.578A pdb=" N CYS D 233 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 245 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS D 250 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 276 through 278 removed outlier: 3.583A pdb=" N LEU D 285 " --> pdb=" O TRP D 297 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.822A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.822A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE N 110 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 142 through 147 removed outlier: 3.871A pdb=" N PHE N 200 " --> pdb=" O CYS N 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER N 192 " --> pdb=" O THR N 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 182 through 183 removed outlier: 6.529A pdb=" N TRP N 164 " --> pdb=" O LEU N 176 " (cutoff:3.500A) 241 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: 1.86 Time building geometry restraints manager: 1.71 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: 2068 1.34 - 1.46: 1277 1.46 - 1.57: 2997 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 6404 Sorted by residual: bond pdb=" C TYR N 223 " pdb=" N PRO N 224 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.83e+00 bond pdb=" CB VAL D 71 " pdb=" CG2 VAL D 71 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 bond pdb=" CD1 TYR N 223 " pdb=" CE1 TYR N 223 " ideal model delta sigma weight residual 1.382 1.348 0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CA TYR N 223 " pdb=" C TYR N 223 " ideal model delta sigma weight residual 1.524 1.537 -0.014 1.26e-02 6.30e+03 1.17e+00 bond pdb=" C ASP N 74 " pdb=" N PRO N 75 " ideal model delta sigma weight residual 1.335 1.348 -0.014 1.28e-02 6.10e+03 1.15e+00 ... (remaining 6399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 8432 1.63 - 3.27: 219 3.27 - 4.90: 35 4.90 - 6.54: 5 6.54 - 8.17: 6 Bond angle restraints: 8697 Sorted by residual: angle pdb=" C PRO C 157 " pdb=" N LEU C 158 " pdb=" CA LEU C 158 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ASP C 85 " pdb=" N VAL C 86 " pdb=" CA VAL C 86 " ideal model delta sigma weight residual 121.97 129.03 -7.06 1.80e+00 3.09e-01 1.54e+01 angle pdb=" C GLU N 222 " pdb=" N TYR N 223 " pdb=" CA TYR N 223 " ideal model delta sigma weight residual 121.80 114.58 7.22 2.44e+00 1.68e-01 8.76e+00 angle pdb=" CA TYR N 223 " pdb=" CB TYR N 223 " pdb=" CG TYR N 223 " ideal model delta sigma weight residual 113.90 108.92 4.98 1.80e+00 3.09e-01 7.64e+00 angle pdb=" CA VAL C 86 " pdb=" CB VAL C 86 " pdb=" CG1 VAL C 86 " ideal model delta sigma weight residual 110.40 114.99 -4.59 1.70e+00 3.46e-01 7.29e+00 ... (remaining 8692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 3446 17.72 - 35.43: 268 35.43 - 53.15: 48 53.15 - 70.86: 5 70.86 - 88.58: 5 Dihedral angle restraints: 3772 sinusoidal: 1357 harmonic: 2415 Sorted by residual: dihedral pdb=" CB CYS N 147 " pdb=" SG CYS N 147 " pdb=" SG CYS N 217 " pdb=" CB CYS N 217 " ideal model delta sinusoidal sigma weight residual 93.00 -178.42 -88.58 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CA GLN N 130 " pdb=" C GLN N 130 " pdb=" N ALA N 131 " pdb=" CA ALA N 131 " ideal model delta harmonic sigma weight residual 180.00 159.33 20.67 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU D 261 " pdb=" C LEU D 261 " pdb=" N MET D 262 " pdb=" CA MET D 262 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 868 0.071 - 0.141: 120 0.141 - 0.212: 3 0.212 - 0.283: 0 0.283 - 0.353: 1 Chirality restraints: 992 Sorted by residual: chirality pdb=" CB VAL C 86 " pdb=" CA VAL C 86 " pdb=" CG1 VAL C 86 " pdb=" CG2 VAL C 86 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CG LEU D 30 " pdb=" CB LEU D 30 " pdb=" CD1 LEU D 30 " pdb=" CD2 LEU D 30 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CA ILE D 229 " pdb=" N ILE D 229 " pdb=" C ILE D 229 " pdb=" CB ILE D 229 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.09e-01 ... (remaining 989 not shown) Planarity restraints: 1120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 235 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO D 236 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 236 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 193 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO D 194 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 194 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 194 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE N 138 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO N 139 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO N 139 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO N 139 " -0.026 5.00e-02 4.00e+02 ... (remaining 1117 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 248 2.71 - 3.26: 5768 3.26 - 3.81: 10207 3.81 - 4.35: 12144 4.35 - 4.90: 21610 Nonbonded interactions: 49977 Sorted by model distance: nonbonded pdb=" OE2 GLU D 260 " pdb=" OG1 THR D 263 " model vdw 2.166 3.040 nonbonded pdb=" OH TYR C 194 " pdb=" OD2 ASP C 215 " model vdw 2.238 3.040 nonbonded pdb=" OG SER N 149 " pdb=" O LYS N 151 " model vdw 2.247 3.040 nonbonded pdb=" OD2 ASP D 170 " pdb=" OG1 THR D 173 " model vdw 2.280 3.040 nonbonded pdb=" O GLY N 33 " pdb=" OG SER N 99 " model vdw 2.296 3.040 ... (remaining 49972 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: 3.440 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.180 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6404 Z= 0.289 Angle : 0.658 8.175 8697 Z= 0.353 Chirality : 0.047 0.353 992 Planarity : 0.004 0.052 1120 Dihedral : 13.245 83.870 2215 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.29), residues: 826 helix: 0.80 (0.42), residues: 141 sheet: -0.82 (0.32), residues: 275 loop : -1.65 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 169 HIS 0.006 0.001 HIS N 220 PHE 0.017 0.002 PHE D 199 TYR 0.022 0.002 TYR N 223 ARG 0.003 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.607 Fit side-chains REVERT: C 9 ASP cc_start: 0.6813 (m-30) cc_final: 0.6409 (m-30) REVERT: C 32 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7894 (mtmm) REVERT: C 145 LYS cc_start: 0.8420 (mmtm) cc_final: 0.8191 (mmtm) REVERT: C 146 LYS cc_start: 0.8020 (ptmt) cc_final: 0.7814 (ptmt) REVERT: C 170 THR cc_start: 0.8628 (p) cc_final: 0.8300 (p) REVERT: C 211 ASP cc_start: 0.7886 (m-30) cc_final: 0.7642 (m-30) REVERT: D 15 LYS cc_start: 0.8075 (pttp) cc_final: 0.7868 (pttp) REVERT: D 49 ARG cc_start: 0.7843 (mpt180) cc_final: 0.7492 (mmt-90) REVERT: D 83 ASP cc_start: 0.7659 (t70) cc_final: 0.7411 (t70) REVERT: D 243 THR cc_start: 0.7431 (m) cc_final: 0.7019 (m) REVERT: D 258 ASP cc_start: 0.6991 (t0) cc_final: 0.6678 (t0) REVERT: D 290 ASP cc_start: 0.6244 (m-30) cc_final: 0.6039 (m-30) REVERT: N 36 TRP cc_start: 0.8359 (m100) cc_final: 0.7681 (m100) REVERT: N 161 TYR cc_start: 0.7564 (m-80) cc_final: 0.7293 (m-80) REVERT: Y 38 MET cc_start: 0.6034 (ptm) cc_final: 0.5830 (mmt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2350 time to fit residues: 42.0460 Evaluate side-chains 132 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 34 optimal weight: 0.0060 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 ASN D 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.158496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136734 restraints weight = 9053.352| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.65 r_work: 0.3656 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6404 Z= 0.245 Angle : 0.560 6.374 8697 Z= 0.300 Chirality : 0.043 0.162 992 Planarity : 0.004 0.044 1120 Dihedral : 4.672 30.862 896 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.24 % Allowed : 7.11 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.30), residues: 826 helix: 1.87 (0.46), residues: 143 sheet: -0.64 (0.32), residues: 281 loop : -1.50 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 211 HIS 0.005 0.001 HIS N 35 PHE 0.018 0.002 PHE D 253 TYR 0.025 0.002 TYR N 223 ARG 0.004 0.000 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: C 32 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8095 (mtmm) REVERT: C 145 LYS cc_start: 0.8491 (mmtm) cc_final: 0.8200 (mmtm) REVERT: C 170 THR cc_start: 0.8442 (p) cc_final: 0.8075 (p) REVERT: C 211 ASP cc_start: 0.7894 (m-30) cc_final: 0.7679 (m-30) REVERT: D 75 GLN cc_start: 0.8043 (mm110) cc_final: 0.7593 (mp10) REVERT: D 243 THR cc_start: 0.7262 (m) cc_final: 0.6814 (m) REVERT: D 258 ASP cc_start: 0.7149 (t0) cc_final: 0.6911 (t0) REVERT: D 293 ASN cc_start: 0.7089 (t0) cc_final: 0.6887 (t0) REVERT: D 298 ASP cc_start: 0.6825 (m-30) cc_final: 0.6405 (m-30) REVERT: N 20 LEU cc_start: 0.7136 (mm) cc_final: 0.6920 (mt) REVERT: N 36 TRP cc_start: 0.8219 (m100) cc_final: 0.7646 (m100) REVERT: N 200 PHE cc_start: 0.8050 (m-80) cc_final: 0.7715 (m-80) outliers start: 8 outliers final: 5 residues processed: 133 average time/residue: 0.2123 time to fit residues: 35.9471 Evaluate side-chains 133 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 329 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 16 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 44 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.158345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.136930 restraints weight = 9218.384| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.59 r_work: 0.3654 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6404 Z= 0.269 Angle : 0.558 6.957 8697 Z= 0.298 Chirality : 0.044 0.175 992 Planarity : 0.004 0.045 1120 Dihedral : 4.655 28.666 896 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.39 % Allowed : 10.82 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.30), residues: 826 helix: 2.06 (0.47), residues: 143 sheet: -0.47 (0.32), residues: 276 loop : -1.48 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 169 HIS 0.005 0.001 HIS N 35 PHE 0.018 0.002 PHE D 253 TYR 0.024 0.002 TYR N 223 ARG 0.005 0.000 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: C 9 ASP cc_start: 0.6799 (m-30) cc_final: 0.6537 (m-30) REVERT: C 32 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8097 (mtmm) REVERT: C 145 LYS cc_start: 0.8459 (mmtm) cc_final: 0.8151 (mmtm) REVERT: C 170 THR cc_start: 0.8504 (p) cc_final: 0.8205 (p) REVERT: C 211 ASP cc_start: 0.7898 (m-30) cc_final: 0.7680 (m-30) REVERT: D 49 ARG cc_start: 0.7677 (mpt180) cc_final: 0.7425 (mmt-90) REVERT: D 75 GLN cc_start: 0.8022 (mm110) cc_final: 0.7609 (mp10) REVERT: N 36 TRP cc_start: 0.8209 (m100) cc_final: 0.7647 (m100) outliers start: 9 outliers final: 6 residues processed: 129 average time/residue: 0.2139 time to fit residues: 35.6814 Evaluate side-chains 130 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain N residue 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 11 optimal weight: 0.3980 chunk 81 optimal weight: 0.0270 chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 59 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 7 optimal weight: 0.1980 overall best weight: 0.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.159075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.137737 restraints weight = 9150.574| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.65 r_work: 0.3682 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6404 Z= 0.170 Angle : 0.505 5.554 8697 Z= 0.272 Chirality : 0.042 0.154 992 Planarity : 0.003 0.041 1120 Dihedral : 4.350 25.686 896 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.16 % Allowed : 12.67 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.31), residues: 826 helix: 2.21 (0.47), residues: 143 sheet: -0.49 (0.31), residues: 285 loop : -1.31 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 169 HIS 0.003 0.001 HIS N 35 PHE 0.010 0.001 PHE D 199 TYR 0.022 0.001 TYR N 223 ARG 0.006 0.000 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: C 145 LYS cc_start: 0.8447 (mmtm) cc_final: 0.8162 (mmtm) REVERT: C 170 THR cc_start: 0.8454 (p) cc_final: 0.8170 (p) REVERT: C 211 ASP cc_start: 0.7926 (m-30) cc_final: 0.7701 (m-30) REVERT: N 36 TRP cc_start: 0.8192 (m100) cc_final: 0.7595 (m100) outliers start: 14 outliers final: 10 residues processed: 125 average time/residue: 0.2191 time to fit residues: 35.1110 Evaluate side-chains 127 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 130 GLN Chi-restraints excluded: chain Y residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 63 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.156925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.135845 restraints weight = 9174.067| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.56 r_work: 0.3657 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6404 Z= 0.277 Angle : 0.549 6.745 8697 Z= 0.293 Chirality : 0.043 0.170 992 Planarity : 0.004 0.044 1120 Dihedral : 4.521 24.709 896 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.16 % Allowed : 13.14 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.31), residues: 826 helix: 2.19 (0.48), residues: 143 sheet: -0.45 (0.32), residues: 277 loop : -1.46 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 211 HIS 0.005 0.001 HIS N 35 PHE 0.016 0.002 PHE D 253 TYR 0.023 0.002 TYR N 223 ARG 0.006 0.001 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: C 9 ASP cc_start: 0.6804 (m-30) cc_final: 0.6556 (m-30) REVERT: C 145 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8144 (mmtm) REVERT: C 170 THR cc_start: 0.8485 (p) cc_final: 0.8210 (p) REVERT: C 211 ASP cc_start: 0.7910 (m-30) cc_final: 0.7697 (m-30) REVERT: N 36 TRP cc_start: 0.8183 (m100) cc_final: 0.7653 (m100) outliers start: 14 outliers final: 9 residues processed: 128 average time/residue: 0.2037 time to fit residues: 33.5285 Evaluate side-chains 130 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain N residue 11 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 81 optimal weight: 0.0010 chunk 76 optimal weight: 0.3980 chunk 21 optimal weight: 0.0370 chunk 57 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 overall best weight: 0.2464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.156564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.135857 restraints weight = 9056.488| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.55 r_work: 0.3673 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6404 Z= 0.184 Angle : 0.508 5.821 8697 Z= 0.271 Chirality : 0.042 0.155 992 Planarity : 0.003 0.041 1120 Dihedral : 4.316 24.599 896 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.01 % Allowed : 13.91 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.31), residues: 826 helix: 2.23 (0.47), residues: 143 sheet: -0.48 (0.32), residues: 277 loop : -1.37 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 169 HIS 0.003 0.001 HIS N 35 PHE 0.019 0.001 PHE C 74 TYR 0.022 0.001 TYR N 223 ARG 0.005 0.000 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: C 9 ASP cc_start: 0.6788 (m-30) cc_final: 0.6543 (m-30) REVERT: C 118 MET cc_start: 0.8428 (tpp) cc_final: 0.7946 (tpp) REVERT: C 145 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8141 (mmtm) REVERT: C 170 THR cc_start: 0.8403 (p) cc_final: 0.8131 (p) REVERT: C 211 ASP cc_start: 0.7926 (m-30) cc_final: 0.7690 (m-30) REVERT: N 36 TRP cc_start: 0.8184 (m100) cc_final: 0.7602 (m100) outliers start: 13 outliers final: 11 residues processed: 129 average time/residue: 0.2077 time to fit residues: 34.2754 Evaluate side-chains 134 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain N residue 11 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.155063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.133969 restraints weight = 9134.838| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.56 r_work: 0.3629 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6404 Z= 0.346 Angle : 0.589 9.824 8697 Z= 0.312 Chirality : 0.045 0.188 992 Planarity : 0.004 0.045 1120 Dihedral : 4.692 26.752 896 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.32 % Allowed : 14.68 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.81 (0.31), residues: 826 helix: 2.12 (0.48), residues: 143 sheet: -0.55 (0.31), residues: 280 loop : -1.52 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 211 HIS 0.005 0.001 HIS N 35 PHE 0.020 0.002 PHE D 253 TYR 0.025 0.002 TYR N 223 ARG 0.006 0.001 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: C 9 ASP cc_start: 0.6884 (m-30) cc_final: 0.6614 (m-30) REVERT: C 145 LYS cc_start: 0.8437 (mmtm) cc_final: 0.8119 (mmtm) REVERT: C 170 THR cc_start: 0.8439 (p) cc_final: 0.8179 (p) REVERT: C 211 ASP cc_start: 0.7969 (m-30) cc_final: 0.7751 (m-30) REVERT: N 36 TRP cc_start: 0.8201 (m100) cc_final: 0.7659 (m100) outliers start: 15 outliers final: 12 residues processed: 131 average time/residue: 0.1989 time to fit residues: 33.9988 Evaluate side-chains 134 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain N residue 11 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 55 optimal weight: 0.0370 chunk 52 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.155124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.134608 restraints weight = 9075.802| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.49 r_work: 0.3656 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6404 Z= 0.226 Angle : 0.538 7.123 8697 Z= 0.288 Chirality : 0.043 0.171 992 Planarity : 0.004 0.042 1120 Dihedral : 4.503 25.580 896 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.70 % Allowed : 16.23 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.77 (0.30), residues: 826 helix: 2.15 (0.48), residues: 143 sheet: -0.53 (0.31), residues: 280 loop : -1.49 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 169 HIS 0.003 0.001 HIS N 35 PHE 0.020 0.001 PHE C 74 TYR 0.024 0.002 TYR N 223 ARG 0.006 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: C 9 ASP cc_start: 0.6813 (m-30) cc_final: 0.6547 (m-30) REVERT: C 118 MET cc_start: 0.8436 (tpp) cc_final: 0.7967 (tpp) REVERT: C 170 THR cc_start: 0.8404 (p) cc_final: 0.8163 (p) REVERT: C 211 ASP cc_start: 0.7930 (m-30) cc_final: 0.7703 (m-30) REVERT: N 36 TRP cc_start: 0.8189 (m100) cc_final: 0.7598 (m100) outliers start: 11 outliers final: 11 residues processed: 122 average time/residue: 0.1993 time to fit residues: 31.8199 Evaluate side-chains 127 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 329 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 79 optimal weight: 0.0020 chunk 41 optimal weight: 0.0470 chunk 37 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 overall best weight: 0.2686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.155826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.135139 restraints weight = 9188.175| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.53 r_work: 0.3664 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6404 Z= 0.198 Angle : 0.526 5.944 8697 Z= 0.282 Chirality : 0.042 0.159 992 Planarity : 0.004 0.043 1120 Dihedral : 4.361 23.728 896 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.85 % Allowed : 16.23 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.31), residues: 826 helix: 2.19 (0.47), residues: 143 sheet: -0.57 (0.31), residues: 284 loop : -1.37 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 169 HIS 0.003 0.001 HIS N 35 PHE 0.013 0.001 PHE D 199 TYR 0.022 0.001 TYR N 223 ARG 0.006 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: C 9 ASP cc_start: 0.6778 (m-30) cc_final: 0.6534 (m-30) REVERT: C 118 MET cc_start: 0.8438 (tpp) cc_final: 0.7970 (tpp) REVERT: C 170 THR cc_start: 0.8404 (p) cc_final: 0.8153 (p) REVERT: C 211 ASP cc_start: 0.7907 (m-30) cc_final: 0.7688 (m-30) REVERT: D 66 ASP cc_start: 0.7304 (p0) cc_final: 0.7015 (p0) REVERT: N 36 TRP cc_start: 0.8186 (m100) cc_final: 0.7588 (m100) outliers start: 12 outliers final: 12 residues processed: 125 average time/residue: 0.2008 time to fit residues: 32.7745 Evaluate side-chains 131 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain N residue 162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 18 optimal weight: 0.0040 chunk 16 optimal weight: 0.3980 chunk 61 optimal weight: 0.0980 chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.2290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 HIS D 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.156281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.135492 restraints weight = 9240.749| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.58 r_work: 0.3667 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6404 Z= 0.181 Angle : 0.518 5.794 8697 Z= 0.276 Chirality : 0.042 0.154 992 Planarity : 0.004 0.042 1120 Dihedral : 4.220 21.810 896 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.57 % Favored : 94.31 % Rotamer: Outliers : 1.70 % Allowed : 16.23 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.31), residues: 826 helix: 2.27 (0.47), residues: 143 sheet: -0.52 (0.31), residues: 285 loop : -1.36 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 169 HIS 0.002 0.001 HIS N 35 PHE 0.019 0.001 PHE C 74 TYR 0.022 0.001 TYR N 223 ARG 0.005 0.000 ARG D 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: C 9 ASP cc_start: 0.6771 (m-30) cc_final: 0.6512 (m-30) REVERT: C 118 MET cc_start: 0.8414 (tpp) cc_final: 0.7943 (tpp) REVERT: C 145 LYS cc_start: 0.8431 (mmtm) cc_final: 0.8140 (mmtm) REVERT: C 170 THR cc_start: 0.8372 (p) cc_final: 0.8134 (p) REVERT: C 211 ASP cc_start: 0.7904 (m-30) cc_final: 0.7689 (m-30) REVERT: D 49 ARG cc_start: 0.7945 (mmt-90) cc_final: 0.7742 (mpt180) REVERT: D 66 ASP cc_start: 0.7376 (p0) cc_final: 0.7089 (p0) REVERT: N 36 TRP cc_start: 0.8165 (m100) cc_final: 0.7556 (m100) outliers start: 11 outliers final: 11 residues processed: 121 average time/residue: 0.2022 time to fit residues: 31.6912 Evaluate side-chains 126 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain N residue 162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 7 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 HIS D 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.155216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.134396 restraints weight = 9306.568| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.59 r_work: 0.3646 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6404 Z= 0.242 Angle : 0.543 6.344 8697 Z= 0.289 Chirality : 0.043 0.162 992 Planarity : 0.004 0.044 1120 Dihedral : 4.336 23.202 896 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 1.85 % Allowed : 16.07 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.63 (0.31), residues: 826 helix: 2.26 (0.47), residues: 143 sheet: -0.49 (0.31), residues: 284 loop : -1.37 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 211 HIS 0.007 0.001 HIS C 196 PHE 0.014 0.001 PHE D 199 TYR 0.022 0.002 TYR N 223 ARG 0.007 0.001 ARG D 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3325.77 seconds wall clock time: 58 minutes 7.13 seconds (3487.13 seconds total)