Starting phenix.real_space_refine on Tue Jul 29 12:34:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ppr_17814/07_2025/8ppr_17814.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ppr_17814/07_2025/8ppr_17814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ppr_17814/07_2025/8ppr_17814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ppr_17814/07_2025/8ppr_17814.map" model { file = "/net/cci-nas-00/data/ceres_data/8ppr_17814/07_2025/8ppr_17814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ppr_17814/07_2025/8ppr_17814.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 49 5.16 5 C 7187 2.51 5 N 1948 2.21 5 O 2170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11354 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 6, 'TRANS': 241} Chain: "M" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1692 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "N" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1767 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 13, 'TRANS': 203} Chain breaks: 1 Chain: "P" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1434 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "F" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "G" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1180 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 140} Chain: "K" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 2048 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 236} Chain: "Z" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 336 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.68, per 1000 atoms: 0.68 Number of scatterers: 11354 At special positions: 0 Unit cell: (78.366, 106.959, 321.936, 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 49 16.00 O 2170 8.00 N 1948 7.00 C 7187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.59 Conformation dependent library (CDL) restraints added in 1.4 seconds 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 73.8% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.830A pdb=" N GLU D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 124 removed outlier: 3.878A pdb=" N ARG D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 153 Proline residue: D 151 - end of helix Processing helix chain 'D' and resid 160 through 186 Processing helix chain 'D' and resid 187 through 193 removed outlier: 3.652A pdb=" N CYS D 191 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 246 removed outlier: 5.633A pdb=" N SER D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU D 204 " --> pdb=" O SER D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 Processing helix chain 'D' and resid 264 through 270 Processing helix chain 'D' and resid 274 through 326 removed outlier: 3.527A pdb=" N LEU D 278 " --> pdb=" O TYR D 274 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 338 removed outlier: 3.746A pdb=" N LYS D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 14 Processing helix chain 'M' and resid 16 through 50 removed outlier: 3.593A pdb=" N CYS M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 89 Processing helix chain 'M' and resid 99 through 106 removed outlier: 4.626A pdb=" N CYS M 104 " --> pdb=" O GLU M 101 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU M 106 " --> pdb=" O LYS M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 169 removed outlier: 3.527A pdb=" N LYS M 129 " --> pdb=" O GLN M 125 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS M 169 " --> pdb=" O VAL M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 205 Processing helix chain 'N' and resid 42 through 59 removed outlier: 3.774A pdb=" N VAL N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG N 55 " --> pdb=" O GLN N 51 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE N 56 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL N 57 " --> pdb=" O CYS N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 63 Processing helix chain 'N' and resid 65 through 68 Processing helix chain 'N' and resid 69 through 86 removed outlier: 3.602A pdb=" N LEU N 73 " --> pdb=" O ARG N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 151 Proline residue: N 130 - end of helix Processing helix chain 'N' and resid 166 through 213 Proline residue: N 192 - end of helix Proline residue: N 209 - end of helix Processing helix chain 'N' and resid 214 through 221 Processing helix chain 'N' and resid 264 through 269 Processing helix chain 'P' and resid 33 through 53 Processing helix chain 'P' and resid 54 through 62 Processing helix chain 'P' and resid 62 through 67 Processing helix chain 'P' and resid 69 through 99 Processing helix chain 'P' and resid 100 through 115 Processing helix chain 'P' and resid 128 through 189 removed outlier: 4.002A pdb=" N SER P 135 " --> pdb=" O LYS P 131 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL P 136 " --> pdb=" O ASP P 132 " (cutoff:3.500A) Proline residue: P 139 - end of helix removed outlier: 3.516A pdb=" N GLN P 161 " --> pdb=" O ALA P 157 " (cutoff:3.500A) Processing helix chain 'P' and resid 189 through 201 removed outlier: 4.571A pdb=" N GLU P 193 " --> pdb=" O ALA P 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 148 Proline residue: F 134 - end of helix Processing helix chain 'F' and resid 181 through 192 Processing helix chain 'G' and resid 81 through 143 Processing helix chain 'G' and resid 194 through 205 removed outlier: 3.620A pdb=" N GLN G 198 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASN G 200 " --> pdb=" O GLU G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 223 removed outlier: 3.517A pdb=" N TYR G 223 " --> pdb=" O THR G 219 " (cutoff:3.500A) Processing helix chain 'K' and resid 2098 through 2130 Processing helix chain 'K' and resid 2150 through 2152 No H-bonds generated for 'chain 'K' and resid 2150 through 2152' Processing helix chain 'K' and resid 2171 through 2175 removed outlier: 3.562A pdb=" N ARG K2175 " --> pdb=" O LYS K2172 " (cutoff:3.500A) Processing helix chain 'K' and resid 2192 through 2209 Processing helix chain 'K' and resid 2211 through 2216 Processing helix chain 'K' and resid 2220 through 2250 removed outlier: 4.618A pdb=" N LYS K2224 " --> pdb=" O HIS K2220 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL K2232 " --> pdb=" O GLU K2228 " (cutoff:3.500A) Processing helix chain 'K' and resid 2251 through 2253 No H-bonds generated for 'chain 'K' and resid 2251 through 2253' Processing helix chain 'K' and resid 2305 through 2316 removed outlier: 3.708A pdb=" N ILE K2309 " --> pdb=" O SER K2305 " (cutoff:3.500A) Processing helix chain 'K' and resid 2321 through 2335 Processing helix chain 'K' and resid 2338 through 2342 removed outlier: 3.513A pdb=" N TYR K2341 " --> pdb=" O CYS K2338 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS K2342 " --> pdb=" O HIS K2339 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 2338 through 2342' Processing helix chain 'Z' and resid 184 through 221 removed outlier: 3.609A pdb=" N GLN Z 207 " --> pdb=" O ARG Z 203 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG Z 208 " --> pdb=" O ASP Z 204 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR Z 209 " --> pdb=" O LYS Z 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 38 through 40 removed outlier: 6.545A pdb=" N VAL N 38 " --> pdb=" O SER N 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 253 through 254 removed outlier: 3.620A pdb=" N MET N 254 " --> pdb=" O TRP K2140 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL K2137 " --> pdb=" O THR K2148 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR K2148 " --> pdb=" O VAL K2137 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU K2139 " --> pdb=" O VAL K2146 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN K2144 " --> pdb=" O SER K2141 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE K2154 " --> pdb=" O PHE K2149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 149 through 151 Processing sheet with id=AA4, first strand: chain 'G' and resid 145 through 149 Processing sheet with id=AA5, first strand: chain 'K' and resid 2255 through 2260 removed outlier: 5.529A pdb=" N LEU K2255 " --> pdb=" O SER K2270 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N SER K2270 " --> pdb=" O LEU K2255 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN K2257 " --> pdb=" O LEU K2268 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU K2279 " --> pdb=" O ASN K2299 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ASN K2299 " --> pdb=" O GLU K2279 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR K2281 " --> pdb=" O ILE K2297 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE K2297 " --> pdb=" O THR K2281 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 2466 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: 3.17 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3040 1.33 - 1.45: 1879 1.45 - 1.57: 6558 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 11553 Sorted by residual: bond pdb=" CG LEU F 97 " pdb=" CD1 LEU F 97 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.01e+01 bond pdb=" C ILE F 133 " pdb=" N PRO F 134 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.38e-02 5.25e+03 4.89e+00 bond pdb=" CG LEU F 97 " pdb=" CD2 LEU F 97 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.30e+00 bond pdb=" CB MET D 292 " pdb=" CG MET D 292 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.35e+00 bond pdb=" CG LEU G 96 " pdb=" CD2 LEU G 96 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.95e+00 ... (remaining 11548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 15369 2.39 - 4.78: 167 4.78 - 7.17: 23 7.17 - 9.56: 3 9.56 - 11.95: 3 Bond angle restraints: 15565 Sorted by residual: angle pdb=" CD1 LEU F 97 " pdb=" CG LEU F 97 " pdb=" CD2 LEU F 97 " ideal model delta sigma weight residual 110.80 101.81 8.99 2.20e+00 2.07e-01 1.67e+01 angle pdb=" CB LEU F 97 " pdb=" CG LEU F 97 " pdb=" CD1 LEU F 97 " ideal model delta sigma weight residual 110.70 99.58 11.12 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C PHE D 305 " pdb=" N MET D 306 " pdb=" CA MET D 306 " ideal model delta sigma weight residual 120.72 114.80 5.92 1.67e+00 3.59e-01 1.26e+01 angle pdb=" CA LEU F 102 " pdb=" CB LEU F 102 " pdb=" CG LEU F 102 " ideal model delta sigma weight residual 116.30 128.25 -11.95 3.50e+00 8.16e-02 1.17e+01 angle pdb=" CB MET D 292 " pdb=" CG MET D 292 " pdb=" SD MET D 292 " ideal model delta sigma weight residual 112.70 103.29 9.41 3.00e+00 1.11e-01 9.85e+00 ... (remaining 15560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 6429 17.50 - 34.99: 606 34.99 - 52.49: 77 52.49 - 69.99: 28 69.99 - 87.48: 13 Dihedral angle restraints: 7153 sinusoidal: 3043 harmonic: 4110 Sorted by residual: dihedral pdb=" CA PHE K2149 " pdb=" C PHE K2149 " pdb=" N VAL K2150 " pdb=" CA VAL K2150 " ideal model delta harmonic sigma weight residual -180.00 -149.46 -30.54 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA ASN K2262 " pdb=" C ASN K2262 " pdb=" N ASN K2263 " pdb=" CA ASN K2263 " ideal model delta harmonic sigma weight residual -180.00 -152.56 -27.44 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA ASP N 253 " pdb=" C ASP N 253 " pdb=" N MET N 254 " pdb=" CA MET N 254 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 7150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1196 0.032 - 0.064: 344 0.064 - 0.096: 131 0.096 - 0.129: 41 0.129 - 0.161: 14 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CB ILE P 32 " pdb=" CA ILE P 32 " pdb=" CG1 ILE P 32 " pdb=" CG2 ILE P 32 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA GLU D 205 " pdb=" N GLU D 205 " pdb=" C GLU D 205 " pdb=" CB GLU D 205 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CB THR P 31 " pdb=" CA THR P 31 " pdb=" OG1 THR P 31 " pdb=" CG2 THR P 31 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 1723 not shown) Planarity restraints: 2019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 133 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO F 134 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO F 134 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 134 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 67 " 0.017 2.00e-02 2.50e+03 1.68e-02 4.96e+00 pdb=" CG PHE M 67 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE M 67 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE M 67 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE M 67 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE M 67 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE M 67 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER M 56 " -0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO M 57 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO M 57 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO M 57 " -0.028 5.00e-02 4.00e+02 ... (remaining 2016 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 187 2.69 - 3.24: 11725 3.24 - 3.79: 18813 3.79 - 4.35: 23420 4.35 - 4.90: 38297 Nonbonded interactions: 92442 Sorted by model distance: nonbonded pdb=" OG SER K2305 " pdb=" OD1 ASP K2307 " model vdw 2.133 3.040 nonbonded pdb=" O ILE F 149 " pdb=" OH TYR G 138 " model vdw 2.155 3.040 nonbonded pdb=" OD1 ASP F 117 " pdb=" NE2 GLN F 121 " model vdw 2.170 3.120 nonbonded pdb=" O ASP F 117 " pdb=" NE2 GLN F 121 " model vdw 2.179 3.120 nonbonded pdb=" OE1 GLU P 203 " pdb=" OH TYR K2245 " model vdw 2.184 3.040 ... (remaining 92437 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: 5.570 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.300 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 11553 Z= 0.148 Angle : 0.630 11.952 15565 Z= 0.331 Chirality : 0.039 0.161 1726 Planarity : 0.005 0.074 2019 Dihedral : 14.029 87.483 4461 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 3.16 (0.23), residues: 1370 helix: 2.98 (0.16), residues: 939 sheet: -1.10 (0.50), residues: 101 loop : 0.54 (0.40), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K2140 HIS 0.007 0.001 HIS K2220 PHE 0.039 0.002 PHE M 67 TYR 0.014 0.001 TYR G 110 ARG 0.013 0.001 ARG K2120 Details of bonding type rmsd hydrogen bonds : bond 0.10479 ( 843) hydrogen bonds : angle 4.89756 ( 2466) covalent geometry : bond 0.00306 (11553) covalent geometry : angle 0.63041 (15565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: D 98 ARG cc_start: 0.6396 (ptm160) cc_final: 0.6041 (ptm160) REVERT: M 1 MET cc_start: 0.3264 (ppp) cc_final: 0.2094 (tpt) REVERT: M 88 GLN cc_start: 0.8986 (tp40) cc_final: 0.8748 (tp40) REVERT: M 92 ARG cc_start: 0.6757 (tpp-160) cc_final: 0.6254 (tpp80) REVERT: M 104 CYS cc_start: 0.9098 (m) cc_final: 0.8034 (t) REVERT: P 38 LEU cc_start: 0.7919 (tt) cc_final: 0.7661 (tt) REVERT: P 131 LYS cc_start: 0.8621 (mppt) cc_final: 0.8160 (tptt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 1.1669 time to fit residues: 167.6204 Evaluate side-chains 91 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.0570 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 GLN D 147 GLN D 231 HIS P 106 ASN ** P 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2221 GLN ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.187177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.125387 restraints weight = 20030.064| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.52 r_work: 0.3551 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11553 Z= 0.176 Angle : 0.592 10.538 15565 Z= 0.308 Chirality : 0.041 0.186 1726 Planarity : 0.004 0.064 2019 Dihedral : 3.989 30.627 1489 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.57 % Allowed : 7.40 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 3.14 (0.23), residues: 1370 helix: 3.00 (0.16), residues: 942 sheet: -1.50 (0.48), residues: 104 loop : 0.55 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 78 HIS 0.007 0.001 HIS D 231 PHE 0.026 0.002 PHE M 67 TYR 0.017 0.002 TYR P 77 ARG 0.009 0.001 ARG M 23 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 843) hydrogen bonds : angle 4.12829 ( 2466) covalent geometry : bond 0.00406 (11553) covalent geometry : angle 0.59184 (15565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: D 98 ARG cc_start: 0.6201 (ptm160) cc_final: 0.5858 (ptm160) REVERT: M 1 MET cc_start: 0.3435 (ppp) cc_final: 0.2298 (tpt) REVERT: M 25 TYR cc_start: 0.8528 (t80) cc_final: 0.8054 (t80) REVERT: M 70 PHE cc_start: 0.7752 (t80) cc_final: 0.7200 (t80) REVERT: M 74 HIS cc_start: 0.8088 (m90) cc_final: 0.7849 (m90) REVERT: M 88 GLN cc_start: 0.9042 (tp40) cc_final: 0.8804 (tp40) REVERT: M 104 CYS cc_start: 0.9381 (m) cc_final: 0.8559 (p) REVERT: P 130 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7541 (tp30) REVERT: G 152 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6775 (tt0) REVERT: K 2142 ASP cc_start: 0.7909 (m-30) cc_final: 0.7604 (m-30) REVERT: K 2225 MET cc_start: 0.8200 (tmm) cc_final: 0.7940 (tmm) outliers start: 20 outliers final: 4 residues processed: 116 average time/residue: 1.3005 time to fit residues: 163.4062 Evaluate side-chains 94 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain G residue 152 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 93 optimal weight: 50.0000 chunk 72 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS M 11 GLN ** P 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.186788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.124021 restraints weight = 20275.801| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.62 r_work: 0.3498 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11553 Z= 0.199 Angle : 0.599 10.335 15565 Z= 0.308 Chirality : 0.041 0.172 1726 Planarity : 0.004 0.056 2019 Dihedral : 4.109 31.339 1489 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.97 % Allowed : 10.62 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.23), residues: 1370 helix: 2.82 (0.16), residues: 942 sheet: -2.00 (0.44), residues: 104 loop : 0.43 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 78 HIS 0.007 0.001 HIS D 231 PHE 0.023 0.002 PHE M 86 TYR 0.019 0.002 TYR P 77 ARG 0.007 0.001 ARG M 23 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 843) hydrogen bonds : angle 4.05240 ( 2466) covalent geometry : bond 0.00466 (11553) covalent geometry : angle 0.59855 (15565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3263 (ppp) cc_final: 0.2353 (tpt) REVERT: M 71 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7844 (mtp) REVERT: M 74 HIS cc_start: 0.8023 (m90) cc_final: 0.7782 (m90) REVERT: M 88 GLN cc_start: 0.8942 (tp40) cc_final: 0.8696 (tp40) REVERT: M 104 CYS cc_start: 0.9369 (m) cc_final: 0.8547 (p) REVERT: P 119 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6639 (tmmm) REVERT: P 130 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7578 (tp30) REVERT: G 129 LYS cc_start: 0.7762 (pptt) cc_final: 0.7336 (ptmt) REVERT: G 152 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6704 (tt0) REVERT: G 164 LYS cc_start: 0.6765 (OUTLIER) cc_final: 0.6415 (mttp) REVERT: K 2142 ASP cc_start: 0.7838 (m-30) cc_final: 0.7533 (m-30) REVERT: Z 212 PHE cc_start: 0.4581 (t80) cc_final: 0.4379 (t80) outliers start: 25 outliers final: 5 residues processed: 111 average time/residue: 1.5543 time to fit residues: 186.9156 Evaluate side-chains 96 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 MET Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 164 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 39 optimal weight: 0.9990 chunk 90 optimal weight: 0.0270 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 86 optimal weight: 0.0970 chunk 98 optimal weight: 0.7980 chunk 131 optimal weight: 50.0000 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS M 11 GLN P 184 GLN ** P 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.188321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.125696 restraints weight = 20141.966| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.63 r_work: 0.3521 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11553 Z= 0.142 Angle : 0.548 11.146 15565 Z= 0.280 Chirality : 0.039 0.162 1726 Planarity : 0.004 0.047 2019 Dihedral : 3.968 30.520 1489 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.05 % Allowed : 12.04 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 3.13 (0.23), residues: 1370 helix: 3.07 (0.16), residues: 940 sheet: -1.99 (0.45), residues: 104 loop : 0.48 (0.39), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 78 HIS 0.007 0.001 HIS D 231 PHE 0.015 0.001 PHE M 86 TYR 0.018 0.001 TYR P 77 ARG 0.007 0.000 ARG M 23 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 843) hydrogen bonds : angle 3.85909 ( 2466) covalent geometry : bond 0.00321 (11553) covalent geometry : angle 0.54799 (15565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3477 (ppp) cc_final: 0.2408 (tpt) REVERT: M 25 TYR cc_start: 0.8516 (t80) cc_final: 0.8002 (t80) REVERT: M 71 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7801 (mtp) REVERT: M 74 HIS cc_start: 0.8243 (m90) cc_final: 0.8017 (m90) REVERT: M 88 GLN cc_start: 0.8992 (tp40) cc_final: 0.8734 (tp40) REVERT: M 92 ARG cc_start: 0.6815 (tpp-160) cc_final: 0.6420 (tpp-160) REVERT: M 104 CYS cc_start: 0.9388 (m) cc_final: 0.8600 (p) REVERT: P 119 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6577 (tmmm) REVERT: P 130 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7586 (tp30) REVERT: G 129 LYS cc_start: 0.7664 (pptt) cc_final: 0.7224 (ptmt) REVERT: G 152 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6712 (tt0) REVERT: G 164 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6696 (mttp) REVERT: K 2142 ASP cc_start: 0.7928 (m-30) cc_final: 0.7620 (m-30) outliers start: 26 outliers final: 7 residues processed: 116 average time/residue: 1.9866 time to fit residues: 250.6279 Evaluate side-chains 100 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain M residue 71 MET Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 164 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 65 optimal weight: 0.0970 chunk 23 optimal weight: 0.0670 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 90 optimal weight: 0.2980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS N 156 HIS ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.189013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.126551 restraints weight = 20090.457| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.63 r_work: 0.3534 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11553 Z= 0.126 Angle : 0.542 12.924 15565 Z= 0.275 Chirality : 0.038 0.204 1726 Planarity : 0.004 0.046 2019 Dihedral : 3.873 28.849 1489 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.28 % Allowed : 12.67 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 3.30 (0.23), residues: 1370 helix: 3.19 (0.16), residues: 940 sheet: -1.83 (0.46), residues: 102 loop : 0.52 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 78 HIS 0.007 0.001 HIS D 231 PHE 0.017 0.001 PHE M 79 TYR 0.020 0.001 TYR P 77 ARG 0.007 0.000 ARG M 23 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 843) hydrogen bonds : angle 3.73441 ( 2466) covalent geometry : bond 0.00276 (11553) covalent geometry : angle 0.54159 (15565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3727 (ppp) cc_final: 0.2581 (tpt) REVERT: M 25 TYR cc_start: 0.8459 (t80) cc_final: 0.7954 (t80) REVERT: M 71 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7752 (mtp) REVERT: M 88 GLN cc_start: 0.8980 (tp40) cc_final: 0.8726 (tp40) REVERT: M 92 ARG cc_start: 0.6913 (tpp-160) cc_final: 0.6557 (tpp-160) REVERT: M 104 CYS cc_start: 0.9365 (m) cc_final: 0.8577 (p) REVERT: N 55 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6276 (mmp-170) REVERT: P 119 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6664 (tmmm) REVERT: P 130 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7602 (tp30) REVERT: G 129 LYS cc_start: 0.7648 (pptt) cc_final: 0.7193 (ptmt) REVERT: G 136 ASP cc_start: 0.8063 (t0) cc_final: 0.7696 (m-30) REVERT: G 164 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6803 (mttp) REVERT: K 2142 ASP cc_start: 0.7934 (m-30) cc_final: 0.7654 (m-30) outliers start: 29 outliers final: 11 residues processed: 112 average time/residue: 1.3943 time to fit residues: 168.9416 Evaluate side-chains 101 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain M residue 71 MET Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 55 ARG Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain K residue 2256 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 20 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 112 optimal weight: 0.2980 chunk 118 optimal weight: 0.0770 chunk 7 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 156 HIS ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.187233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.124086 restraints weight = 20159.506| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.63 r_work: 0.3495 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11553 Z= 0.174 Angle : 0.584 12.690 15565 Z= 0.297 Chirality : 0.040 0.201 1726 Planarity : 0.004 0.047 2019 Dihedral : 3.976 29.230 1489 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.44 % Allowed : 13.77 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 3.06 (0.23), residues: 1370 helix: 3.04 (0.16), residues: 932 sheet: -2.16 (0.45), residues: 104 loop : 0.51 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 78 HIS 0.008 0.001 HIS D 231 PHE 0.017 0.002 PHE G 210 TYR 0.021 0.001 TYR P 77 ARG 0.013 0.000 ARG M 23 Details of bonding type rmsd hydrogen bonds : bond 0.04544 ( 843) hydrogen bonds : angle 3.88349 ( 2466) covalent geometry : bond 0.00404 (11553) covalent geometry : angle 0.58385 (15565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3634 (ppp) cc_final: 0.2016 (tpt) REVERT: M 25 TYR cc_start: 0.8452 (t80) cc_final: 0.7951 (t80) REVERT: M 92 ARG cc_start: 0.6998 (tpp-160) cc_final: 0.6495 (tpp-160) REVERT: M 104 CYS cc_start: 0.9354 (m) cc_final: 0.8501 (p) REVERT: N 55 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6334 (mmp-170) REVERT: N 170 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7369 (mpp) REVERT: P 95 ILE cc_start: 0.5405 (OUTLIER) cc_final: 0.5168 (tp) REVERT: P 119 LYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6649 (tmmm) REVERT: P 130 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7630 (tp30) REVERT: G 136 ASP cc_start: 0.8016 (t0) cc_final: 0.7720 (m-30) REVERT: G 164 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6829 (mttp) REVERT: K 2142 ASP cc_start: 0.7929 (m-30) cc_final: 0.7634 (m-30) outliers start: 31 outliers final: 11 residues processed: 110 average time/residue: 1.3364 time to fit residues: 160.9673 Evaluate side-chains 97 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain M residue 70 PHE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 55 ARG Chi-restraints excluded: chain N residue 170 MET Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain G residue 199 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 36 optimal weight: 0.0870 chunk 123 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 92 optimal weight: 0.0970 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 156 HIS ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.187931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.125245 restraints weight = 20350.490| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.64 r_work: 0.3513 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11553 Z= 0.144 Angle : 0.553 13.116 15565 Z= 0.283 Chirality : 0.039 0.163 1726 Planarity : 0.004 0.046 2019 Dihedral : 3.920 29.435 1489 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.36 % Allowed : 14.24 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 3.18 (0.23), residues: 1370 helix: 3.12 (0.16), residues: 937 sheet: -2.10 (0.46), residues: 102 loop : 0.52 (0.39), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K2212 HIS 0.012 0.001 HIS M 74 PHE 0.015 0.001 PHE M 79 TYR 0.022 0.001 TYR P 77 ARG 0.012 0.000 ARG M 23 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 843) hydrogen bonds : angle 3.78071 ( 2466) covalent geometry : bond 0.00327 (11553) covalent geometry : angle 0.55333 (15565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3236 (ppp) cc_final: 0.1630 (tpt) REVERT: M 25 TYR cc_start: 0.8562 (t80) cc_final: 0.7984 (t80) REVERT: M 92 ARG cc_start: 0.6951 (tpp-160) cc_final: 0.6725 (tpp-160) REVERT: M 104 CYS cc_start: 0.9351 (m) cc_final: 0.8505 (p) REVERT: N 55 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.6327 (mmp-170) REVERT: N 170 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7324 (mmm) REVERT: P 119 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6638 (tmmm) REVERT: P 130 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7631 (tp30) REVERT: G 136 ASP cc_start: 0.7995 (t0) cc_final: 0.7718 (m-30) REVERT: G 164 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6821 (mttp) REVERT: K 2142 ASP cc_start: 0.7932 (m-30) cc_final: 0.7648 (m-30) outliers start: 30 outliers final: 13 residues processed: 112 average time/residue: 1.2825 time to fit residues: 156.4239 Evaluate side-chains 102 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 55 ARG Chi-restraints excluded: chain N residue 170 MET Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain K residue 2297 ILE Chi-restraints excluded: chain K residue 2337 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 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 231 HIS ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 GLN ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.186781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.123781 restraints weight = 20217.742| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.63 r_work: 0.3482 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11553 Z= 0.172 Angle : 0.588 13.307 15565 Z= 0.300 Chirality : 0.040 0.154 1726 Planarity : 0.004 0.047 2019 Dihedral : 3.993 29.119 1489 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.20 % Allowed : 14.87 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 3.00 (0.23), residues: 1370 helix: 3.00 (0.16), residues: 931 sheet: -2.23 (0.45), residues: 103 loop : 0.49 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K2212 HIS 0.009 0.001 HIS D 231 PHE 0.015 0.002 PHE G 210 TYR 0.025 0.002 TYR P 77 ARG 0.012 0.000 ARG M 23 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 843) hydrogen bonds : angle 3.88700 ( 2466) covalent geometry : bond 0.00403 (11553) covalent geometry : angle 0.58767 (15565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3151 (ppp) cc_final: 0.1861 (tpt) REVERT: M 25 TYR cc_start: 0.8548 (t80) cc_final: 0.7945 (t80) REVERT: M 92 ARG cc_start: 0.6947 (tpp-160) cc_final: 0.6704 (tpp-160) REVERT: N 170 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7347 (mmm) REVERT: P 119 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6684 (tmmm) REVERT: P 130 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: G 136 ASP cc_start: 0.7977 (t0) cc_final: 0.7703 (m-30) REVERT: G 164 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6834 (mttp) REVERT: K 2142 ASP cc_start: 0.7941 (m-30) cc_final: 0.7640 (m-30) outliers start: 28 outliers final: 18 residues processed: 110 average time/residue: 1.2544 time to fit residues: 150.2052 Evaluate side-chains 105 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain M residue 70 PHE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 55 ARG Chi-restraints excluded: chain N residue 170 MET Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain K residue 2137 VAL Chi-restraints excluded: chain K residue 2297 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 51 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 108 optimal weight: 50.0000 chunk 16 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 91 optimal weight: 0.0050 chunk 57 optimal weight: 0.0980 chunk 131 optimal weight: 50.0000 chunk 66 optimal weight: 0.6980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.187980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.125903 restraints weight = 20118.629| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.54 r_work: 0.3535 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11553 Z= 0.136 Angle : 0.562 13.368 15565 Z= 0.286 Chirality : 0.038 0.172 1726 Planarity : 0.004 0.046 2019 Dihedral : 3.929 29.098 1489 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.97 % Allowed : 15.66 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 3.19 (0.23), residues: 1370 helix: 3.12 (0.16), residues: 936 sheet: -2.02 (0.46), residues: 101 loop : 0.51 (0.39), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K2212 HIS 0.009 0.001 HIS D 231 PHE 0.013 0.001 PHE M 79 TYR 0.025 0.001 TYR P 77 ARG 0.011 0.000 ARG M 23 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 843) hydrogen bonds : angle 3.77176 ( 2466) covalent geometry : bond 0.00304 (11553) covalent geometry : angle 0.56195 (15565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3213 (ppp) cc_final: 0.1964 (tpt) REVERT: M 25 TYR cc_start: 0.8548 (t80) cc_final: 0.7962 (t80) REVERT: M 92 ARG cc_start: 0.7004 (tpp-160) cc_final: 0.6741 (tpp-160) REVERT: M 104 CYS cc_start: 0.9365 (m) cc_final: 0.8547 (p) REVERT: N 104 MET cc_start: 0.7181 (pmm) cc_final: 0.6551 (pmm) REVERT: N 170 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7219 (mmm) REVERT: P 109 ASP cc_start: 0.8656 (m-30) cc_final: 0.8407 (p0) REVERT: P 119 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6653 (tmmm) REVERT: P 130 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7595 (tp30) REVERT: G 136 ASP cc_start: 0.7962 (t0) cc_final: 0.7689 (m-30) REVERT: G 164 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6793 (mttp) REVERT: K 2142 ASP cc_start: 0.7918 (m-30) cc_final: 0.7583 (m-30) outliers start: 25 outliers final: 13 residues processed: 108 average time/residue: 1.2841 time to fit residues: 152.7029 Evaluate side-chains 100 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 170 MET Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain K residue 2297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 64 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 16 optimal weight: 0.0270 chunk 89 optimal weight: 1.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.187817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.125576 restraints weight = 20029.039| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.53 r_work: 0.3528 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11553 Z= 0.141 Angle : 0.585 14.318 15565 Z= 0.295 Chirality : 0.039 0.165 1726 Planarity : 0.004 0.046 2019 Dihedral : 3.934 29.026 1489 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.81 % Allowed : 15.89 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 3.17 (0.23), residues: 1370 helix: 3.10 (0.16), residues: 936 sheet: -1.96 (0.47), residues: 101 loop : 0.51 (0.39), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K2212 HIS 0.010 0.001 HIS D 231 PHE 0.022 0.002 PHE M 70 TYR 0.026 0.001 TYR P 77 ARG 0.010 0.000 ARG M 23 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 843) hydrogen bonds : angle 3.78137 ( 2466) covalent geometry : bond 0.00318 (11553) covalent geometry : angle 0.58533 (15565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3265 (ppp) cc_final: 0.1992 (tpt) REVERT: M 25 TYR cc_start: 0.8607 (t80) cc_final: 0.8045 (t80) REVERT: M 92 ARG cc_start: 0.6974 (tpp-160) cc_final: 0.6709 (tpp-160) REVERT: M 104 CYS cc_start: 0.9366 (m) cc_final: 0.8542 (p) REVERT: N 104 MET cc_start: 0.7184 (pmm) cc_final: 0.6556 (pmm) REVERT: N 170 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7225 (mmm) REVERT: P 109 ASP cc_start: 0.8648 (m-30) cc_final: 0.8436 (p0) REVERT: P 119 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6631 (tmmm) REVERT: P 130 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7603 (tp30) REVERT: G 136 ASP cc_start: 0.7945 (t0) cc_final: 0.7675 (m-30) REVERT: G 164 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6796 (mttp) REVERT: K 2142 ASP cc_start: 0.7911 (m-30) cc_final: 0.7602 (m-30) outliers start: 23 outliers final: 15 residues processed: 103 average time/residue: 1.3390 time to fit residues: 151.7825 Evaluate side-chains 103 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 170 MET Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain K residue 2297 ILE Chi-restraints excluded: chain K residue 2337 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 88 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.182157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.119019 restraints weight = 20211.455| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.48 r_work: 0.3527 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11553 Z= 0.163 Angle : 0.599 13.578 15565 Z= 0.303 Chirality : 0.039 0.168 1726 Planarity : 0.004 0.047 2019 Dihedral : 4.045 29.021 1489 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.81 % Allowed : 16.05 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 3.05 (0.23), residues: 1370 helix: 3.01 (0.16), residues: 931 sheet: -2.05 (0.47), residues: 101 loop : 0.50 (0.39), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K2212 HIS 0.010 0.001 HIS D 231 PHE 0.024 0.002 PHE M 70 TYR 0.026 0.002 TYR P 77 ARG 0.010 0.000 ARG M 23 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 843) hydrogen bonds : angle 3.86057 ( 2466) covalent geometry : bond 0.00379 (11553) covalent geometry : angle 0.59894 (15565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11541.96 seconds wall clock time: 212 minutes 44.28 seconds (12764.28 seconds total)