Starting phenix.real_space_refine on Sat Jul 20 16:01:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppr_17814/07_2024/8ppr_17814.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppr_17814/07_2024/8ppr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppr_17814/07_2024/8ppr_17814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppr_17814/07_2024/8ppr_17814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppr_17814/07_2024/8ppr_17814.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppr_17814/07_2024/8ppr_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 Residue "P GLU 90": "OE1" <-> "OE2" Residue "F ASP 117": "OD1" <-> "OD2" Residue "G PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 7.21, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 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: 4.33 Conformation dependent library (CDL) restraints added in 1.9 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: 0.98 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: 4.77 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: 96.59 - 104.06: 137 104.06 - 111.54: 5231 111.54 - 119.01: 4242 119.01 - 126.49: 5824 126.49 - 133.97: 131 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 2.440 nonbonded pdb=" O ILE F 149 " pdb=" OH TYR G 138 " model vdw 2.155 2.440 nonbonded pdb=" OD1 ASP F 117 " pdb=" NE2 GLN F 121 " model vdw 2.170 2.520 nonbonded pdb=" O ASP F 117 " pdb=" NE2 GLN F 121 " model vdw 2.179 2.520 nonbonded pdb=" OE1 GLU P 203 " pdb=" OH TYR K2245 " model vdw 2.184 2.440 ... (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 ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.660 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: 0.090 Set scattering table: 0.100 Process input model: 31.790 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.120 ------------------------------------------------------------------------------- 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= 0.205 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.290 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: 1.1448 time to fit residues: 164.8401 Evaluate side-chains 91 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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: 0.7980 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 231 HIS M 11 GLN M 194 ASN ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11553 Z= 0.335 Angle : 0.613 10.411 15565 Z= 0.317 Chirality : 0.042 0.182 1726 Planarity : 0.004 0.069 2019 Dihedral : 4.046 31.264 1489 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.19 % Favored : 97.74 % Rotamer: Outliers : 1.81 % Allowed : 7.63 % Favored : 90.56 % 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: 2.99 (0.23), residues: 1370 helix: 2.92 (0.16), residues: 940 sheet: -1.60 (0.48), residues: 104 loop : 0.43 (0.39), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 78 HIS 0.007 0.002 HIS K2234 PHE 0.026 0.002 PHE M 67 TYR 0.017 0.002 TYR G 138 ARG 0.011 0.001 ARG M 23 *********************** 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 123 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 1.320 Fit side-chains REVERT: D 98 ARG cc_start: 0.6311 (ptm160) cc_final: 0.6026 (ptm160) REVERT: M 1 MET cc_start: 0.3262 (ppp) cc_final: 0.1702 (tpt) REVERT: M 25 TYR cc_start: 0.8492 (t80) cc_final: 0.8070 (t80) REVERT: M 74 HIS cc_start: 0.7751 (m90) cc_final: 0.7546 (m90) REVERT: M 104 CYS cc_start: 0.9125 (m) cc_final: 0.8059 (t) REVERT: N 254 MET cc_start: 0.3569 (ttm) cc_final: 0.3356 (ttt) REVERT: G 152 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6196 (tt0) outliers start: 23 outliers final: 6 residues processed: 113 average time/residue: 1.2493 time to fit residues: 153.4054 Evaluate side-chains 92 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 87 SER Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 204 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 82 optimal weight: 50.0000 chunk 33 optimal weight: 0.3980 chunk 121 optimal weight: 0.5980 chunk 131 optimal weight: 50.0000 chunk 108 optimal weight: 50.0000 chunk 120 optimal weight: 0.0980 chunk 41 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 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 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS M 194 ASN ** P 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11553 Z= 0.238 Angle : 0.550 10.557 15565 Z= 0.281 Chirality : 0.039 0.179 1726 Planarity : 0.004 0.057 2019 Dihedral : 4.003 32.146 1489 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.61 % Favored : 98.32 % Rotamer: Outliers : 1.89 % Allowed : 10.70 % 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: 3.09 (0.23), residues: 1370 helix: 3.03 (0.16), residues: 941 sheet: -1.85 (0.46), residues: 104 loop : 0.45 (0.39), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 78 HIS 0.007 0.001 HIS D 231 PHE 0.022 0.002 PHE M 86 TYR 0.018 0.002 TYR P 77 ARG 0.006 0.000 ARG M 23 *********************** 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 116 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: M 1 MET cc_start: 0.3055 (ppp) cc_final: 0.1594 (tpt) REVERT: M 25 TYR cc_start: 0.8462 (t80) cc_final: 0.8021 (t80) REVERT: M 71 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7607 (mtp) REVERT: M 74 HIS cc_start: 0.7901 (m90) cc_final: 0.7624 (m90) REVERT: M 104 CYS cc_start: 0.9104 (m) cc_final: 0.8081 (t) REVERT: P 119 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6717 (tmmm) REVERT: G 152 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6158 (tt0) outliers start: 24 outliers final: 8 residues processed: 106 average time/residue: 1.2233 time to fit residues: 141.2176 Evaluate side-chains 98 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain K residue 2256 MET Chi-restraints excluded: chain K residue 2337 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 0.3980 chunk 129 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 107 optimal weight: 50.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS M 194 ASN ** P 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K2204 GLN K2263 ASN ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11553 Z= 0.268 Angle : 0.562 11.458 15565 Z= 0.286 Chirality : 0.039 0.149 1726 Planarity : 0.004 0.051 2019 Dihedral : 4.024 30.494 1489 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % Rotamer: Outliers : 2.36 % Allowed : 12.12 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 2.99 (0.16), residues: 936 sheet: -2.01 (0.47), residues: 104 loop : 0.40 (0.39), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 78 HIS 0.006 0.001 HIS D 231 PHE 0.015 0.002 PHE G 210 TYR 0.019 0.002 TYR P 77 ARG 0.007 0.000 ARG M 23 *********************** 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 119 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 89 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: M 1 MET cc_start: 0.3528 (ppp) cc_final: 0.1904 (tpt) REVERT: M 71 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7624 (mtp) REVERT: M 74 HIS cc_start: 0.7888 (m90) cc_final: 0.7639 (m90) REVERT: M 104 CYS cc_start: 0.9117 (m) cc_final: 0.8081 (t) REVERT: P 119 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6655 (tmmm) REVERT: G 152 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6164 (tt0) outliers start: 30 outliers final: 10 residues processed: 108 average time/residue: 1.2080 time to fit residues: 142.3196 Evaluate side-chains 94 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 70 PHE 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 178 LEU Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain K residue 2337 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS D 233 GLN M 194 ASN ** P 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11553 Z= 0.425 Angle : 0.663 12.103 15565 Z= 0.337 Chirality : 0.043 0.152 1726 Planarity : 0.005 0.053 2019 Dihedral : 4.335 32.124 1489 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.15 % Rotamer: Outliers : 3.23 % Allowed : 13.53 % Favored : 83.24 % 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: 2.43 (0.23), residues: 1370 helix: 2.57 (0.16), residues: 941 sheet: -2.33 (0.46), residues: 104 loop : 0.16 (0.39), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K2212 HIS 0.008 0.002 HIS K2234 PHE 0.028 0.002 PHE G 210 TYR 0.019 0.002 TYR D 232 ARG 0.006 0.001 ARG K2173 *********************** 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 129 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 88 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.3091 (ppp) cc_final: 0.1424 (tpt) REVERT: M 23 ARG cc_start: 0.8112 (ttp-170) cc_final: 0.7766 (ttp-170) REVERT: M 71 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7743 (mtp) REVERT: M 74 HIS cc_start: 0.8020 (m90) cc_final: 0.7751 (m90) REVERT: M 104 CYS cc_start: 0.9126 (m) cc_final: 0.7984 (t) REVERT: P 58 PHE cc_start: 0.6287 (OUTLIER) cc_final: 0.5709 (t80) REVERT: P 95 ILE cc_start: 0.5694 (OUTLIER) cc_final: 0.5443 (tp) REVERT: P 119 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6683 (tmmm) REVERT: G 152 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6335 (tt0) outliers start: 41 outliers final: 15 residues processed: 121 average time/residue: 1.1417 time to fit residues: 151.0866 Evaluate side-chains 103 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 70 PHE Chi-restraints excluded: chain M residue 71 MET Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 95 ILE 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 178 LEU Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain K residue 2137 VAL Chi-restraints excluded: chain K residue 2297 ILE Chi-restraints excluded: chain K residue 2337 ASP Chi-restraints excluded: chain Z residue 213 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 107 optimal weight: 50.0000 chunk 60 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 42 optimal weight: 0.2980 chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS M 194 ASN ** P 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11553 Z= 0.249 Angle : 0.574 12.254 15565 Z= 0.291 Chirality : 0.039 0.183 1726 Planarity : 0.004 0.049 2019 Dihedral : 4.127 32.092 1489 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.26 % Favored : 97.66 % Rotamer: Outliers : 2.75 % Allowed : 14.63 % Favored : 82.61 % 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: 2.76 (0.23), residues: 1370 helix: 2.80 (0.16), residues: 941 sheet: -2.05 (0.48), residues: 95 loop : 0.18 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K2212 HIS 0.006 0.001 HIS D 231 PHE 0.017 0.002 PHE M 86 TYR 0.017 0.001 TYR K2151 ARG 0.006 0.000 ARG D 98 *********************** 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 123 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 98 ARG cc_start: 0.6064 (tmm-80) cc_final: 0.5509 (tmm-80) REVERT: M 1 MET cc_start: 0.3142 (ppp) cc_final: 0.1903 (tpt) REVERT: M 23 ARG cc_start: 0.8108 (ttp-170) cc_final: 0.7764 (ttp-170) REVERT: M 25 TYR cc_start: 0.8726 (t80) cc_final: 0.8208 (t80) REVERT: M 104 CYS cc_start: 0.9148 (m) cc_final: 0.8130 (t) REVERT: P 58 PHE cc_start: 0.6038 (OUTLIER) cc_final: 0.5469 (t80) REVERT: P 95 ILE cc_start: 0.5385 (OUTLIER) cc_final: 0.5105 (tp) REVERT: P 119 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6692 (tmmm) REVERT: G 152 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6235 (tt0) outliers start: 35 outliers final: 17 residues processed: 115 average time/residue: 1.0685 time to fit residues: 135.2992 Evaluate side-chains 106 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 287 CYS 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 N residue 264 CYS Chi-restraints excluded: chain P residue 58 PHE 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 178 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain K residue 2137 VAL Chi-restraints excluded: chain K residue 2297 ILE Chi-restraints excluded: chain K residue 2337 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 94 optimal weight: 30.0000 chunk 109 optimal weight: 50.0000 chunk 72 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 79 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS M 194 ASN ** P 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11553 Z= 0.267 Angle : 0.590 12.925 15565 Z= 0.299 Chirality : 0.040 0.192 1726 Planarity : 0.004 0.046 2019 Dihedral : 4.122 31.296 1489 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.34 % Favored : 97.59 % Rotamer: Outliers : 2.91 % Allowed : 15.74 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 2.76 (0.23), residues: 1370 helix: 2.82 (0.16), residues: 936 sheet: -2.09 (0.48), residues: 95 loop : 0.20 (0.39), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K2212 HIS 0.006 0.001 HIS D 231 PHE 0.021 0.002 PHE N 115 TYR 0.024 0.002 TYR P 77 ARG 0.006 0.000 ARG D 98 *********************** 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 128 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 91 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 242 ARG cc_start: 0.5747 (OUTLIER) cc_final: 0.5457 (ttm170) REVERT: M 1 MET cc_start: 0.3136 (ppp) cc_final: 0.1884 (tpt) REVERT: M 25 TYR cc_start: 0.8726 (t80) cc_final: 0.8153 (t80) REVERT: M 104 CYS cc_start: 0.9132 (m) cc_final: 0.8073 (t) REVERT: N 55 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.6012 (mmp-170) REVERT: P 58 PHE cc_start: 0.5984 (OUTLIER) cc_final: 0.5519 (t80) REVERT: P 119 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6681 (tmmm) REVERT: G 192 GLU cc_start: 0.5821 (OUTLIER) cc_final: 0.5214 (mp0) outliers start: 37 outliers final: 21 residues processed: 117 average time/residue: 1.1932 time to fit residues: 153.1836 Evaluate side-chains 111 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain M residue 69 CYS 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 N residue 55 ARG Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 58 PHE 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 173 VAL Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain K residue 2136 ASP Chi-restraints excluded: chain K residue 2137 VAL 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 77 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 82 optimal weight: 50.0000 chunk 87 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 117 optimal weight: 0.0770 chunk 123 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 GLN D 231 HIS ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 194 ASN ** P 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11553 Z= 0.195 Angle : 0.571 13.449 15565 Z= 0.288 Chirality : 0.039 0.204 1726 Planarity : 0.004 0.044 2019 Dihedral : 4.011 31.212 1489 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.04 % Favored : 97.88 % Rotamer: Outliers : 2.83 % Allowed : 15.97 % Favored : 81.20 % 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: 3.01 (0.23), residues: 1370 helix: 3.01 (0.16), residues: 934 sheet: -1.95 (0.49), residues: 95 loop : 0.30 (0.38), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K2135 HIS 0.008 0.001 HIS K2339 PHE 0.024 0.001 PHE N 115 TYR 0.025 0.001 TYR N 129 ARG 0.009 0.000 ARG M 23 *********************** 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 130 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 94 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 242 ARG cc_start: 0.5772 (OUTLIER) cc_final: 0.5486 (ttm170) REVERT: M 1 MET cc_start: 0.3234 (ppp) cc_final: 0.1957 (tpt) REVERT: M 25 TYR cc_start: 0.8696 (t80) cc_final: 0.8117 (t80) REVERT: M 104 CYS cc_start: 0.9129 (m) cc_final: 0.8144 (t) REVERT: N 55 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.6104 (mmp-170) REVERT: P 58 PHE cc_start: 0.5961 (OUTLIER) cc_final: 0.5538 (t80) REVERT: P 119 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6684 (tmmm) outliers start: 36 outliers final: 18 residues processed: 119 average time/residue: 1.0833 time to fit residues: 142.2967 Evaluate side-chains 112 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 287 CYS 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 119 ILE Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 73 THR 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 173 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain K residue 2297 ILE Chi-restraints excluded: chain K residue 2337 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 50.0000 chunk 36 optimal weight: 0.5980 chunk 108 optimal weight: 50.0000 chunk 113 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 127 optimal weight: 0.4980 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 231 HIS M 194 ASN ** P 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11553 Z= 0.282 Angle : 0.610 13.627 15565 Z= 0.308 Chirality : 0.040 0.203 1726 Planarity : 0.004 0.059 2019 Dihedral : 4.113 30.388 1489 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.37 % Rotamer: Outliers : 2.91 % Allowed : 16.44 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 2.82 (0.23), residues: 1370 helix: 2.85 (0.16), residues: 934 sheet: -2.02 (0.49), residues: 95 loop : 0.27 (0.38), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K2135 HIS 0.009 0.001 HIS M 74 PHE 0.016 0.002 PHE G 210 TYR 0.025 0.002 TYR P 77 ARG 0.011 0.000 ARG M 23 *********************** 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 125 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 88 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 242 ARG cc_start: 0.5774 (OUTLIER) cc_final: 0.5483 (ttm170) REVERT: M 1 MET cc_start: 0.3268 (ppp) cc_final: 0.2046 (tpt) REVERT: M 25 TYR cc_start: 0.8698 (t80) cc_final: 0.8178 (t80) REVERT: M 104 CYS cc_start: 0.9099 (m) cc_final: 0.8021 (t) REVERT: P 58 PHE cc_start: 0.5979 (OUTLIER) cc_final: 0.2068 (t80) REVERT: P 77 TYR cc_start: 0.6304 (t80) cc_final: 0.6045 (m-10) REVERT: P 119 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6678 (tmmm) REVERT: G 192 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5336 (mm-30) outliers start: 37 outliers final: 19 residues processed: 115 average time/residue: 0.9881 time to fit residues: 125.6106 Evaluate side-chains 106 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 287 CYS 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 264 CYS Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 73 THR 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 173 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain K residue 2137 VAL Chi-restraints excluded: chain K residue 2297 ILE Chi-restraints excluded: chain K residue 2326 VAL 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 77 optimal weight: 0.3980 chunk 60 optimal weight: 0.0980 chunk 88 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 122 optimal weight: 0.3980 chunk 106 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 82 optimal weight: 50.0000 chunk 65 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS M 194 ASN N 208 GLN ** P 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11553 Z= 0.188 Angle : 0.591 13.684 15565 Z= 0.299 Chirality : 0.040 0.357 1726 Planarity : 0.004 0.067 2019 Dihedral : 4.009 31.307 1489 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.34 % Favored : 97.59 % Rotamer: Outliers : 2.05 % Allowed : 17.62 % Favored : 80.33 % 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: 3.01 (0.23), residues: 1370 helix: 3.00 (0.16), residues: 939 sheet: -1.81 (0.51), residues: 95 loop : 0.21 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K2135 HIS 0.009 0.001 HIS D 231 PHE 0.032 0.002 PHE M 28 TYR 0.029 0.001 TYR N 129 ARG 0.010 0.000 ARG M 23 ********************** 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 115 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 242 ARG cc_start: 0.5677 (OUTLIER) cc_final: 0.5400 (ttm170) REVERT: M 1 MET cc_start: 0.3001 (ppp) cc_final: 0.1758 (tpt) REVERT: M 21 MET cc_start: 0.8084 (mmm) cc_final: 0.7285 (mmm) REVERT: M 104 CYS cc_start: 0.9116 (m) cc_final: 0.8153 (t) REVERT: N 208 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: P 58 PHE cc_start: 0.5964 (OUTLIER) cc_final: 0.2007 (t80) REVERT: P 77 TYR cc_start: 0.6501 (t80) cc_final: 0.6107 (m-10) REVERT: P 119 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6668 (tmmm) outliers start: 26 outliers final: 14 residues processed: 109 average time/residue: 1.0159 time to fit residues: 122.5284 Evaluate side-chains 105 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 287 CYS 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 208 GLN Chi-restraints excluded: chain N residue 264 CYS Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 98 GLU Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain K residue 2297 ILE Chi-restraints excluded: chain K residue 2326 VAL 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 32 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 93 optimal weight: 50.0000 chunk 6 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS M 194 ASN N 208 GLN ** P 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.183498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.120407 restraints weight = 19708.167| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.66 r_work: 0.3476 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11553 Z= 0.313 Angle : 0.642 13.669 15565 Z= 0.326 Chirality : 0.042 0.290 1726 Planarity : 0.004 0.056 2019 Dihedral : 4.157 30.503 1489 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.37 % Rotamer: Outliers : 1.97 % Allowed : 17.62 % Favored : 80.41 % 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: 2.73 (0.23), residues: 1370 helix: 2.78 (0.16), residues: 933 sheet: -2.00 (0.50), residues: 95 loop : 0.25 (0.38), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K2135 HIS 0.010 0.001 HIS D 231 PHE 0.030 0.002 PHE M 28 TYR 0.030 0.002 TYR N 129 ARG 0.014 0.000 ARG M 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3675.70 seconds wall clock time: 66 minutes 18.46 seconds (3978.46 seconds total)