Starting phenix.real_space_refine on Fri Dec 27 17:56:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iec_35378/12_2024/8iec_35378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iec_35378/12_2024/8iec_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_35378/12_2024/8iec_35378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iec_35378/12_2024/8iec_35378.map" model { file = "/net/cci-nas-00/data/ceres_data/8iec_35378/12_2024/8iec_35378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iec_35378/12_2024/8iec_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-5532/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: 4.89, 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: 1.55 Conformation dependent library (CDL) restraints added in 957.5 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: 0.82 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: 1.92 Time building geometry restraints manager: 1.80 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: 0.010 Normalize map: mean=0, sd=1: 4.250 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: 0.040 Set scattering table: 0.060 Process input model: 18.970 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.300 ------------------------------------------------------------------------------- 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 : 0.620 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: 0.2340 time to fit residues: 41.6720 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 : 0.656 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 : 0.663 Fit side-chains revert: symmetry clash REVERT: C 32 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7889 (mtmm) REVERT: C 118 MET cc_start: 0.8542 (tpp) cc_final: 0.8306 (tpp) REVERT: C 145 LYS cc_start: 0.8440 (mmtm) cc_final: 0.8145 (mmtm) REVERT: C 170 THR cc_start: 0.8429 (p) cc_final: 0.8041 (p) REVERT: C 211 ASP cc_start: 0.7924 (m-30) cc_final: 0.7701 (m-30) REVERT: D 15 LYS cc_start: 0.8083 (pttp) cc_final: 0.7843 (pttp) REVERT: D 75 GLN cc_start: 0.8150 (mm110) cc_final: 0.7622 (mp10) REVERT: D 83 ASP cc_start: 0.7824 (t70) cc_final: 0.7574 (t70) REVERT: D 243 THR cc_start: 0.7233 (m) cc_final: 0.6777 (m) REVERT: D 258 ASP cc_start: 0.7161 (t0) cc_final: 0.6877 (t0) REVERT: D 293 ASN cc_start: 0.7137 (t0) cc_final: 0.6924 (t0) REVERT: D 298 ASP cc_start: 0.6848 (m-30) cc_final: 0.6417 (m-30) REVERT: N 20 LEU cc_start: 0.7160 (mm) cc_final: 0.6926 (mt) REVERT: N 36 TRP cc_start: 0.8384 (m100) cc_final: 0.7779 (m100) REVERT: N 200 PHE cc_start: 0.8206 (m-80) cc_final: 0.7817 (m-80) outliers start: 8 outliers final: 5 residues processed: 133 average time/residue: 0.2168 time to fit residues: 36.5825 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 : 0.730 ------------------------------------------------------------------------------- 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 41 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6404 Z= 0.338 Angle : 0.589 7.331 8697 Z= 0.313 Chirality : 0.045 0.184 992 Planarity : 0.004 0.047 1120 Dihedral : 4.815 29.119 896 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.39 % Allowed : 11.28 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.30), residues: 826 helix: 2.02 (0.47), residues: 143 sheet: -0.51 (0.32), residues: 277 loop : -1.52 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 211 HIS 0.005 0.001 HIS N 35 PHE 0.022 0.002 PHE D 253 TYR 0.025 0.002 TYR N 223 ARG 0.004 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 133 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: C 9 ASP cc_start: 0.7042 (m-30) cc_final: 0.6667 (m-30) REVERT: C 24 LYS cc_start: 0.7113 (mmtp) cc_final: 0.6899 (mmtp) REVERT: C 32 LYS cc_start: 0.8188 (mtmm) cc_final: 0.7957 (mtmm) REVERT: C 145 LYS cc_start: 0.8423 (mmtm) cc_final: 0.8111 (mmtm) REVERT: C 170 THR cc_start: 0.8487 (p) cc_final: 0.8179 (p) REVERT: C 211 ASP cc_start: 0.7985 (m-30) cc_final: 0.7754 (m-30) REVERT: D 15 LYS cc_start: 0.8071 (pttp) cc_final: 0.7859 (pttp) REVERT: D 49 ARG cc_start: 0.7796 (mpt180) cc_final: 0.7406 (mmt-90) REVERT: D 75 GLN cc_start: 0.8163 (mm110) cc_final: 0.7655 (mp10) REVERT: D 83 ASP cc_start: 0.7871 (t70) cc_final: 0.7604 (t70) REVERT: N 36 TRP cc_start: 0.8351 (m100) cc_final: 0.7788 (m100) outliers start: 9 outliers final: 6 residues processed: 127 average time/residue: 0.2006 time to fit residues: 32.9796 Evaluate side-chains 128 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 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 73 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.0980 chunk 79 optimal weight: 0.0370 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 overall best weight: 0.2458 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6404 Z= 0.194 Angle : 0.517 5.830 8697 Z= 0.278 Chirality : 0.042 0.163 992 Planarity : 0.004 0.042 1120 Dihedral : 4.481 26.606 896 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.01 % Allowed : 12.98 % Favored : 85.01 % 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: -0.66 (0.31), residues: 826 helix: 2.18 (0.48), residues: 143 sheet: -0.47 (0.31), residues: 279 loop : -1.39 (0.31), residues: 404 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 0.017 0.001 PHE C 74 TYR 0.023 0.001 TYR N 223 ARG 0.005 0.000 ARG D 219 *********************** 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: 13 poor density : 122 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: C 24 LYS cc_start: 0.7084 (mmtp) cc_final: 0.6874 (mmtp) REVERT: C 145 LYS cc_start: 0.8402 (mmtm) cc_final: 0.8096 (mmtm) REVERT: C 170 THR cc_start: 0.8431 (p) cc_final: 0.8138 (p) REVERT: C 211 ASP cc_start: 0.7990 (m-30) cc_final: 0.7761 (m-30) REVERT: D 15 LYS cc_start: 0.8098 (pttp) cc_final: 0.7874 (pttp) REVERT: D 49 ARG cc_start: 0.7742 (mpt180) cc_final: 0.7486 (mmt-90) REVERT: D 83 ASP cc_start: 0.7782 (t70) cc_final: 0.7546 (t70) REVERT: D 179 THR cc_start: 0.8140 (m) cc_final: 0.7924 (t) REVERT: N 36 TRP cc_start: 0.8339 (m100) cc_final: 0.7731 (m100) outliers start: 13 outliers final: 8 residues processed: 127 average time/residue: 0.2052 time to fit residues: 33.4210 Evaluate side-chains 129 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 165 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 59 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6404 Z= 0.369 Angle : 0.594 7.393 8697 Z= 0.317 Chirality : 0.045 0.190 992 Planarity : 0.004 0.047 1120 Dihedral : 4.826 27.837 896 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.47 % Allowed : 13.45 % 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: -0.79 (0.31), residues: 826 helix: 2.08 (0.48), residues: 143 sheet: -0.50 (0.32), residues: 278 loop : -1.52 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 211 HIS 0.005 0.001 HIS N 35 PHE 0.021 0.002 PHE D 253 TYR 0.025 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 143 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: C 9 ASP cc_start: 0.7066 (m-30) cc_final: 0.6693 (m-30) REVERT: C 24 LYS cc_start: 0.7118 (mmtp) cc_final: 0.6918 (mmtp) REVERT: C 145 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8104 (mmtm) REVERT: C 170 THR cc_start: 0.8446 (p) cc_final: 0.8166 (p) REVERT: C 211 ASP cc_start: 0.8022 (m-30) cc_final: 0.7794 (m-30) REVERT: D 15 LYS cc_start: 0.8071 (pttp) cc_final: 0.7853 (pttp) REVERT: D 49 ARG cc_start: 0.7788 (mpt180) cc_final: 0.7410 (mmt-90) REVERT: D 83 ASP cc_start: 0.7846 (t70) cc_final: 0.7612 (t70) REVERT: D 165 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7784 (t) REVERT: N 36 TRP cc_start: 0.8333 (m100) cc_final: 0.7782 (m100) outliers start: 16 outliers final: 9 residues processed: 133 average time/residue: 0.1915 time to fit residues: 33.2447 Evaluate side-chains 134 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 165 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 162 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.0970 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6404 Z= 0.319 Angle : 0.569 6.971 8697 Z= 0.304 Chirality : 0.044 0.190 992 Planarity : 0.004 0.045 1120 Dihedral : 4.777 28.274 896 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.85 % Allowed : 15.46 % Favored : 82.69 % 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: -0.85 (0.30), residues: 826 helix: 2.08 (0.48), residues: 143 sheet: -0.64 (0.31), residues: 280 loop : -1.49 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 211 HIS 0.004 0.001 HIS N 35 PHE 0.019 0.002 PHE C 74 TYR 0.026 0.002 TYR N 223 ARG 0.006 0.000 ARG D 197 *********************** 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: 12 poor density : 124 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: C 9 ASP cc_start: 0.7063 (m-30) cc_final: 0.6693 (m-30) REVERT: C 24 LYS cc_start: 0.7065 (mmtp) cc_final: 0.6861 (mmtp) REVERT: C 145 LYS cc_start: 0.8406 (mmtm) cc_final: 0.8098 (mmtm) REVERT: C 170 THR cc_start: 0.8439 (p) cc_final: 0.8169 (p) REVERT: C 211 ASP cc_start: 0.8014 (m-30) cc_final: 0.7791 (m-30) REVERT: D 15 LYS cc_start: 0.8069 (pttp) cc_final: 0.7834 (pttp) REVERT: D 49 ARG cc_start: 0.7772 (mpt180) cc_final: 0.7463 (mmt-90) REVERT: D 83 ASP cc_start: 0.7839 (t70) cc_final: 0.7591 (t70) REVERT: N 36 TRP cc_start: 0.8342 (m100) cc_final: 0.7759 (m100) outliers start: 12 outliers final: 10 residues processed: 128 average time/residue: 0.2015 time to fit residues: 33.4329 Evaluate side-chains 132 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 165 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 162 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 44 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6404 Z= 0.261 Angle : 0.550 6.813 8697 Z= 0.294 Chirality : 0.043 0.180 992 Planarity : 0.004 0.046 1120 Dihedral : 4.658 27.636 896 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.70 % Allowed : 16.85 % Favored : 81.45 % 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: -0.84 (0.30), residues: 826 helix: 2.13 (0.48), residues: 143 sheet: -0.68 (0.31), residues: 285 loop : -1.47 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 169 HIS 0.004 0.001 HIS N 35 PHE 0.017 0.001 PHE D 199 TYR 0.025 0.002 TYR N 223 ARG 0.006 0.000 ARG D 197 *********************** 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 132 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: C 9 ASP cc_start: 0.7035 (m-30) cc_final: 0.6669 (m-30) REVERT: C 145 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8094 (mmtm) REVERT: C 170 THR cc_start: 0.8405 (p) cc_final: 0.8140 (p) REVERT: C 211 ASP cc_start: 0.8011 (m-30) cc_final: 0.7789 (m-30) REVERT: D 15 LYS cc_start: 0.8046 (pttp) cc_final: 0.7816 (pttp) REVERT: D 49 ARG cc_start: 0.7783 (mpt180) cc_final: 0.7507 (mmt-90) REVERT: D 83 ASP cc_start: 0.7805 (t70) cc_final: 0.7562 (t70) REVERT: D 165 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7316 (p) REVERT: D 179 THR cc_start: 0.8216 (m) cc_final: 0.8003 (t) REVERT: N 36 TRP cc_start: 0.8339 (m100) cc_final: 0.7743 (m100) outliers start: 11 outliers final: 8 residues processed: 126 average time/residue: 0.2075 time to fit residues: 33.5857 Evaluate side-chains 128 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 165 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 162 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.0010 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 chunk 75 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 overall best weight: 0.3964 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6404 Z= 0.248 Angle : 0.542 7.552 8697 Z= 0.289 Chirality : 0.043 0.174 992 Planarity : 0.004 0.044 1120 Dihedral : 4.568 26.174 896 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.16 % Allowed : 16.54 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.16 (0.48), residues: 143 sheet: -0.68 (0.31), residues: 285 loop : -1.44 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 169 HIS 0.004 0.001 HIS N 35 PHE 0.021 0.002 PHE C 74 TYR 0.025 0.002 TYR N 223 ARG 0.006 0.000 ARG D 197 *********************** 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 132 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: C 9 ASP cc_start: 0.7023 (m-30) cc_final: 0.6661 (m-30) REVERT: C 118 MET cc_start: 0.8530 (tpp) cc_final: 0.8021 (tpp) REVERT: C 145 LYS cc_start: 0.8414 (mmtm) cc_final: 0.8095 (mmtm) REVERT: C 170 THR cc_start: 0.8398 (p) cc_final: 0.8131 (p) REVERT: C 211 ASP cc_start: 0.8008 (m-30) cc_final: 0.7783 (m-30) REVERT: D 15 LYS cc_start: 0.8071 (pttp) cc_final: 0.7815 (pttp) REVERT: D 49 ARG cc_start: 0.7797 (mpt180) cc_final: 0.7534 (mmt-90) REVERT: D 83 ASP cc_start: 0.7799 (t70) cc_final: 0.7508 (t70) REVERT: D 165 THR cc_start: 0.7978 (OUTLIER) cc_final: 0.7307 (p) REVERT: D 179 THR cc_start: 0.8207 (m) cc_final: 0.8000 (t) REVERT: N 36 TRP cc_start: 0.8325 (m100) cc_final: 0.7725 (m100) outliers start: 14 outliers final: 11 residues processed: 125 average time/residue: 0.2050 time to fit residues: 33.0869 Evaluate side-chains 129 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 165 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6404 Z= 0.311 Angle : 0.577 7.637 8697 Z= 0.306 Chirality : 0.044 0.189 992 Planarity : 0.004 0.046 1120 Dihedral : 4.710 26.720 896 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.99 % Favored : 91.89 % Rotamer: Outliers : 2.32 % Allowed : 16.85 % Favored : 80.83 % 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: -0.86 (0.30), residues: 826 helix: 2.09 (0.48), residues: 143 sheet: -0.70 (0.31), residues: 286 loop : -1.46 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 211 HIS 0.004 0.001 HIS N 35 PHE 0.017 0.002 PHE D 199 TYR 0.025 0.002 TYR N 223 ARG 0.006 0.001 ARG D 197 *********************** 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 137 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: C 9 ASP cc_start: 0.7041 (m-30) cc_final: 0.6673 (m-30) REVERT: C 145 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8093 (mmtm) REVERT: C 170 THR cc_start: 0.8412 (p) cc_final: 0.8154 (p) REVERT: C 196 HIS cc_start: 0.7378 (t-90) cc_final: 0.7144 (t70) REVERT: C 211 ASP cc_start: 0.8014 (m-30) cc_final: 0.7798 (m-30) REVERT: D 15 LYS cc_start: 0.8046 (pttp) cc_final: 0.7815 (pttp) REVERT: D 49 ARG cc_start: 0.7799 (mpt180) cc_final: 0.7480 (mmt-90) REVERT: D 83 ASP cc_start: 0.7804 (t70) cc_final: 0.7508 (t70) REVERT: N 36 TRP cc_start: 0.8337 (m100) cc_final: 0.7747 (m100) outliers start: 15 outliers final: 14 residues processed: 130 average time/residue: 0.2271 time to fit residues: 38.0279 Evaluate side-chains 133 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 229 ILE 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 Chi-restraints excluded: chain Y residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 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 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 6404 Z= 0.385 Angle : 0.623 8.007 8697 Z= 0.329 Chirality : 0.046 0.206 992 Planarity : 0.004 0.046 1120 Dihedral : 4.978 27.842 896 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.47 % Favored : 91.40 % Rotamer: Outliers : 2.16 % Allowed : 16.85 % Favored : 80.99 % 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: -0.97 (0.30), residues: 826 helix: 1.96 (0.48), residues: 143 sheet: -0.72 (0.31), residues: 280 loop : -1.55 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 169 HIS 0.005 0.001 HIS N 35 PHE 0.022 0.002 PHE C 74 TYR 0.027 0.002 TYR N 223 ARG 0.006 0.001 ARG D 314 ********************** 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 138 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: C 9 ASP cc_start: 0.7062 (m-30) cc_final: 0.6701 (m-30) REVERT: C 145 LYS cc_start: 0.8399 (mmtm) cc_final: 0.8069 (mmtm) REVERT: C 170 THR cc_start: 0.8432 (p) cc_final: 0.8186 (p) REVERT: C 196 HIS cc_start: 0.7410 (t-90) cc_final: 0.7173 (t70) REVERT: C 211 ASP cc_start: 0.8035 (m-30) cc_final: 0.7802 (m-30) REVERT: D 15 LYS cc_start: 0.8054 (pttp) cc_final: 0.7824 (pttp) REVERT: D 83 ASP cc_start: 0.7834 (t70) cc_final: 0.7575 (t70) REVERT: D 165 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7305 (p) REVERT: N 36 TRP cc_start: 0.8337 (m100) cc_final: 0.7760 (m100) outliers start: 14 outliers final: 11 residues processed: 132 average time/residue: 0.1998 time to fit residues: 34.2359 Evaluate side-chains 135 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 229 ILE 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 Y residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.2980 chunk 9 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 65 optimal weight: 0.0770 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 47 optimal weight: 0.0980 overall best weight: 0.1938 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.158110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137274 restraints weight = 9071.903| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.53 r_work: 0.3660 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6404 Z= 0.181 Angle : 0.550 6.731 8697 Z= 0.292 Chirality : 0.043 0.164 992 Planarity : 0.004 0.044 1120 Dihedral : 4.529 25.543 896 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.57 % Favored : 94.31 % Rotamer: Outliers : 1.85 % Allowed : 17.93 % Favored : 80.22 % 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: -0.78 (0.31), residues: 826 helix: 2.19 (0.48), residues: 143 sheet: -0.68 (0.31), residues: 286 loop : -1.40 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 169 HIS 0.003 0.001 HIS D 225 PHE 0.013 0.001 PHE D 199 TYR 0.025 0.001 TYR N 223 ARG 0.005 0.001 ARG D 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1875.14 seconds wall clock time: 35 minutes 17.26 seconds (2117.26 seconds total)