Starting phenix.real_space_refine on Mon Mar 11 04:47:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d9h_7835/03_2024/6d9h_7835_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d9h_7835/03_2024/6d9h_7835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d9h_7835/03_2024/6d9h_7835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d9h_7835/03_2024/6d9h_7835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d9h_7835/03_2024/6d9h_7835_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d9h_7835/03_2024/6d9h_7835_updated.pdb" } resolution = 3.6 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= 0.001 sd= 0.016 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 52 5.16 5 C 4503 2.51 5 N 1196 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7023 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1691 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 206} Chain breaks: 3 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2295 Unusual residues: {'ADN%rna3p': 1} Classifications: {'peptide': 288, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {'PTRANS': 14, 'TRANS': 273, None: 1} Not linked: pdbres="LYS R 301 " pdbres="ADN R 400 " Chain breaks: 1 Time building chain proxies: 4.18, per 1000 atoms: 0.60 Number of scatterers: 7023 At special positions: 0 Unit cell: (76.32, 139.92, 100.7, 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 52 16.00 O 1272 8.00 N 1196 7.00 C 4503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 80 " - pdb=" SG CYS R 169 " distance=2.03 Simple disulfide: pdb=" SG CYS R 260 " - pdb=" SG CYS R 263 " distance=2.03 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: 2.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 9 sheets defined 44.6% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 12 through 31 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 209 through 216 removed outlier: 5.019A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N CYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 216 " --> pdb=" O TRP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.689A pdb=" N TYR A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.909A pdb=" N THR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 331 through 352 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.937A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'R' and resid 7 through 36 Proline residue: R 25 - end of helix Processing helix chain 'R' and resid 43 through 71 removed outlier: 4.860A pdb=" N ILE R 63 " --> pdb=" O GLY R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'R' and resid 77 through 110 Proline residue: R 86 - end of helix removed outlier: 3.623A pdb=" N SER R 93 " --> pdb=" O ILE R 89 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL R 109 " --> pdb=" O ARG R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 118 No H-bonds generated for 'chain 'R' and resid 115 through 118' Processing helix chain 'R' and resid 121 through 144 Proline residue: R 142 - end of helix Processing helix chain 'R' and resid 149 through 159 Processing helix chain 'R' and resid 171 through 174 No H-bonds generated for 'chain 'R' and resid 171 through 174' Processing helix chain 'R' and resid 177 through 187 removed outlier: 3.891A pdb=" N ASN R 184 " --> pdb=" O MET R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 212 Processing helix chain 'R' and resid 224 through 259 removed outlier: 3.610A pdb=" N LEU R 248 " --> pdb=" O ALA R 244 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 267 through 288 removed outlier: 4.437A pdb=" N SER R 281 " --> pdb=" O THR R 277 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA R 282 " --> pdb=" O HIS R 278 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing helix chain 'R' and resid 293 through 300 Processing sheet with id= A, first strand: chain 'A' and resid 320 through 324 removed outlier: 6.929A pdb=" N ILE A 265 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N HIS A 323 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 267 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.072A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.742A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.294A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.835A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.004A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.774A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.885A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 74 through 76 359 hydrogen bonds defined for protein. 1053 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: 2.04 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2229 1.34 - 1.46: 1578 1.46 - 1.58: 3283 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 7165 Sorted by residual: bond pdb=" C VAL R 24 " pdb=" N PRO R 25 " ideal model delta sigma weight residual 1.335 1.364 -0.028 1.36e-02 5.41e+03 4.32e+00 bond pdb=" C THR R 141 " pdb=" N PRO R 142 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.54e+00 bond pdb=" C CYS R 85 " pdb=" N PRO R 86 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.19e-02 7.06e+03 3.20e+00 bond pdb=" CA CYS R 85 " pdb=" C CYS R 85 " ideal model delta sigma weight residual 1.524 1.546 -0.022 1.26e-02 6.30e+03 3.15e+00 bond pdb=" CG LEU B 192 " pdb=" CD1 LEU B 192 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.09e+00 ... (remaining 7160 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.44: 111 105.44 - 112.58: 3713 112.58 - 119.72: 2363 119.72 - 126.87: 3423 126.87 - 134.01: 96 Bond angle restraints: 9706 Sorted by residual: angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 130.04 -8.50 1.91e+00 2.74e-01 1.98e+01 angle pdb=" CA LYS R 35 " pdb=" CB LYS R 35 " pdb=" CG LYS R 35 " ideal model delta sigma weight residual 114.10 122.70 -8.60 2.00e+00 2.50e-01 1.85e+01 angle pdb=" C ILE R 274 " pdb=" N PHE R 275 " pdb=" CA PHE R 275 " ideal model delta sigma weight residual 121.14 113.92 7.22 1.75e+00 3.27e-01 1.70e+01 angle pdb=" N LEU R 248 " pdb=" CA LEU R 248 " pdb=" C LEU R 248 " ideal model delta sigma weight residual 113.16 118.55 -5.39 1.42e+00 4.96e-01 1.44e+01 angle pdb=" C PHE G 61 " pdb=" N ARG G 62 " pdb=" CA ARG G 62 " ideal model delta sigma weight residual 121.70 128.51 -6.81 1.80e+00 3.09e-01 1.43e+01 ... (remaining 9701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 4095 15.22 - 30.44: 145 30.44 - 45.66: 43 45.66 - 60.88: 6 60.88 - 76.10: 4 Dihedral angle restraints: 4293 sinusoidal: 1691 harmonic: 2602 Sorted by residual: dihedral pdb=" CA GLY A 293 " pdb=" C GLY A 293 " pdb=" N ALA A 294 " pdb=" CA ALA A 294 " ideal model delta harmonic sigma weight residual 180.00 -154.06 -25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 4290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 837 0.058 - 0.116: 231 0.116 - 0.174: 45 0.174 - 0.232: 10 0.232 - 0.291: 2 Chirality restraints: 1125 Sorted by residual: chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA PHE R 275 " pdb=" N PHE R 275 " pdb=" C PHE R 275 " pdb=" CB PHE R 275 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA LYS R 35 " pdb=" N LYS R 35 " pdb=" C LYS R 35 " pdb=" CB LYS R 35 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1122 not shown) Planarity restraints: 1213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 181 " 0.025 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C VAL R 181 " -0.087 2.00e-02 2.50e+03 pdb=" O VAL R 181 " 0.032 2.00e-02 2.50e+03 pdb=" N TYR R 182 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 182 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C TYR R 182 " 0.057 2.00e-02 2.50e+03 pdb=" O TYR R 182 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE R 183 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 146 " 0.025 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP R 146 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP R 146 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP R 146 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 146 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 146 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP R 146 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 146 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 146 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 146 " 0.018 2.00e-02 2.50e+03 ... (remaining 1210 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 777 2.76 - 3.29: 6690 3.29 - 3.83: 11452 3.83 - 4.36: 13023 4.36 - 4.90: 23120 Nonbonded interactions: 55062 Sorted by model distance: nonbonded pdb=" OD1 ASP R 55 " pdb=" OG SER R 281 " model vdw 2.219 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.263 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.282 2.440 nonbonded pdb=" O ILE B 123 " pdb=" OG SER B 136 " model vdw 2.298 2.440 nonbonded pdb=" OG1 THR R 44 " pdb=" OD2 ASP R 104 " model vdw 2.335 2.440 ... (remaining 55057 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 group one per residue 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: 0.310 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: 1.660 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.820 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.006 0.084 7165 Z= 0.408 Angle : 0.932 9.857 9706 Z= 0.518 Chirality : 0.056 0.291 1125 Planarity : 0.007 0.050 1213 Dihedral : 9.574 76.099 2595 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.25), residues: 876 helix: 0.08 (0.23), residues: 404 sheet: -0.57 (0.39), residues: 154 loop : -2.65 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP R 146 HIS 0.007 0.002 HIS B 311 PHE 0.039 0.004 PHE R 171 TYR 0.021 0.003 TYR R 179 ARG 0.008 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8049 (m-40) cc_final: 0.7667 (m110) REVERT: B 118 ASP cc_start: 0.7416 (p0) cc_final: 0.7065 (t0) REVERT: R 89 ILE cc_start: 0.8617 (mt) cc_final: 0.8365 (mt) REVERT: R 117 MET cc_start: 0.7175 (ptm) cc_final: 0.6941 (mmm) REVERT: R 275 PHE cc_start: 0.8534 (p90) cc_final: 0.7706 (p90) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1915 time to fit residues: 47.6001 Evaluate side-chains 127 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN B 6 GLN B 88 ASN B 266 HIS R 38 GLN R 184 ASN R 251 HIS R 280 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7165 Z= 0.167 Angle : 0.502 5.973 9706 Z= 0.272 Chirality : 0.041 0.169 1125 Planarity : 0.004 0.040 1213 Dihedral : 5.615 55.157 976 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.58 % Allowed : 9.86 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.28), residues: 876 helix: 1.49 (0.26), residues: 405 sheet: -0.28 (0.39), residues: 155 loop : -2.12 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 188 HIS 0.002 0.001 HIS B 266 PHE 0.040 0.002 PHE R 275 TYR 0.018 0.001 TYR G 40 ARG 0.009 0.000 ARG R 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8254 (t0) REVERT: B 118 ASP cc_start: 0.7536 (p0) cc_final: 0.7177 (t0) REVERT: B 297 TRP cc_start: 0.8746 (m100) cc_final: 0.8247 (m100) REVERT: R 117 MET cc_start: 0.7184 (ptm) cc_final: 0.6909 (mmm) REVERT: R 178 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: R 275 PHE cc_start: 0.8565 (p90) cc_final: 0.8199 (p90) outliers start: 12 outliers final: 8 residues processed: 140 average time/residue: 0.1885 time to fit residues: 35.2788 Evaluate side-chains 132 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 178 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7165 Z= 0.162 Angle : 0.479 7.262 9706 Z= 0.257 Chirality : 0.040 0.163 1125 Planarity : 0.004 0.044 1213 Dihedral : 5.299 53.791 976 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.84 % Allowed : 10.38 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.29), residues: 876 helix: 1.97 (0.26), residues: 408 sheet: -0.06 (0.40), residues: 154 loop : -1.85 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 188 HIS 0.002 0.000 HIS R 251 PHE 0.033 0.001 PHE R 275 TYR 0.007 0.001 TYR A 291 ARG 0.003 0.000 ARG R 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8204 (m110) cc_final: 0.7654 (m-40) REVERT: B 297 TRP cc_start: 0.8727 (m100) cc_final: 0.8345 (m100) REVERT: R 117 MET cc_start: 0.7237 (ptm) cc_final: 0.6969 (mmm) REVERT: R 178 GLU cc_start: 0.7652 (pt0) cc_final: 0.7344 (mt-10) REVERT: R 275 PHE cc_start: 0.8490 (p90) cc_final: 0.8272 (p90) outliers start: 14 outliers final: 10 residues processed: 152 average time/residue: 0.2039 time to fit residues: 40.6987 Evaluate side-chains 135 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7165 Z= 0.267 Angle : 0.528 5.889 9706 Z= 0.287 Chirality : 0.043 0.161 1125 Planarity : 0.004 0.048 1213 Dihedral : 5.657 58.319 976 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.89 % Allowed : 11.04 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.29), residues: 876 helix: 1.86 (0.26), residues: 406 sheet: -0.35 (0.38), residues: 166 loop : -1.94 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 188 HIS 0.004 0.001 HIS A 189 PHE 0.028 0.002 PHE R 275 TYR 0.010 0.001 TYR B 124 ARG 0.007 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8176 (ttpp) REVERT: B 85 TYR cc_start: 0.7510 (m-80) cc_final: 0.7203 (m-80) REVERT: B 88 ASN cc_start: 0.8280 (m110) cc_final: 0.7674 (m-40) REVERT: B 105 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.8562 (t80) REVERT: B 118 ASP cc_start: 0.7855 (p0) cc_final: 0.7185 (t0) REVERT: B 123 ILE cc_start: 0.8726 (mm) cc_final: 0.8487 (mt) REVERT: B 188 MET cc_start: 0.7998 (mmm) cc_final: 0.7783 (mmm) REVERT: B 297 TRP cc_start: 0.8757 (m100) cc_final: 0.8254 (m-10) REVERT: R 178 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7397 (mt-10) outliers start: 22 outliers final: 16 residues processed: 143 average time/residue: 0.1994 time to fit residues: 38.1574 Evaluate side-chains 140 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 57 optimal weight: 0.0870 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7165 Z= 0.159 Angle : 0.454 5.436 9706 Z= 0.247 Chirality : 0.040 0.140 1125 Planarity : 0.003 0.043 1213 Dihedral : 5.230 54.865 976 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.76 % Allowed : 12.61 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.29), residues: 876 helix: 2.19 (0.26), residues: 407 sheet: -0.18 (0.39), residues: 157 loop : -1.73 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 188 HIS 0.002 0.001 HIS B 183 PHE 0.023 0.001 PHE R 275 TYR 0.008 0.001 TYR B 124 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8136 (ttpp) REVERT: A 330 THR cc_start: 0.7613 (OUTLIER) cc_final: 0.7395 (m) REVERT: B 85 TYR cc_start: 0.7520 (m-80) cc_final: 0.7315 (m-80) REVERT: B 88 ASN cc_start: 0.8267 (m110) cc_final: 0.7709 (m-40) REVERT: B 118 ASP cc_start: 0.7867 (p0) cc_final: 0.6999 (t0) REVERT: B 123 ILE cc_start: 0.8751 (mm) cc_final: 0.8529 (mt) REVERT: B 297 TRP cc_start: 0.8798 (m100) cc_final: 0.8421 (m-10) REVERT: R 152 VAL cc_start: 0.7775 (t) cc_final: 0.7575 (p) REVERT: R 178 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7457 (mt-10) outliers start: 21 outliers final: 17 residues processed: 142 average time/residue: 0.1893 time to fit residues: 36.0698 Evaluate side-chains 142 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 78 HIS Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7165 Z= 0.166 Angle : 0.463 9.440 9706 Z= 0.248 Chirality : 0.040 0.139 1125 Planarity : 0.003 0.042 1213 Dihedral : 5.105 53.262 976 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.15 % Allowed : 12.61 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.29), residues: 876 helix: 2.24 (0.26), residues: 413 sheet: -0.17 (0.38), residues: 159 loop : -1.68 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 188 HIS 0.002 0.001 HIS A 189 PHE 0.021 0.001 PHE R 275 TYR 0.009 0.001 TYR B 124 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8299 (m110) cc_final: 0.7744 (m-40) REVERT: B 105 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8571 (t80) REVERT: B 118 ASP cc_start: 0.7848 (p0) cc_final: 0.6942 (t0) REVERT: B 123 ILE cc_start: 0.8779 (mm) cc_final: 0.8569 (mt) REVERT: B 297 TRP cc_start: 0.8792 (m100) cc_final: 0.8463 (m-10) REVERT: R 152 VAL cc_start: 0.7835 (t) cc_final: 0.7581 (p) REVERT: R 178 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7463 (mt-10) outliers start: 24 outliers final: 20 residues processed: 138 average time/residue: 0.1891 time to fit residues: 35.1319 Evaluate side-chains 144 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 78 HIS Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7165 Z= 0.359 Angle : 0.573 7.956 9706 Z= 0.307 Chirality : 0.044 0.139 1125 Planarity : 0.004 0.046 1213 Dihedral : 5.787 60.155 976 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.55 % Allowed : 12.61 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.29), residues: 876 helix: 1.75 (0.26), residues: 418 sheet: -0.37 (0.38), residues: 165 loop : -1.78 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 211 HIS 0.005 0.001 HIS A 189 PHE 0.018 0.002 PHE R 275 TYR 0.010 0.001 TYR R 179 ARG 0.003 0.000 ARG R 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ASP cc_start: 0.7411 (t70) cc_final: 0.7089 (m-30) REVERT: B 68 ARG cc_start: 0.8045 (ttt90) cc_final: 0.7829 (ttt90) REVERT: B 75 GLN cc_start: 0.7498 (tt0) cc_final: 0.7263 (tt0) REVERT: B 88 ASN cc_start: 0.8379 (m110) cc_final: 0.7810 (m-40) REVERT: B 105 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8583 (t80) REVERT: B 118 ASP cc_start: 0.7980 (p0) cc_final: 0.7106 (t0) REVERT: B 123 ILE cc_start: 0.8823 (mm) cc_final: 0.8621 (mt) REVERT: B 164 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8528 (p) REVERT: R 144 PHE cc_start: 0.6664 (m-80) cc_final: 0.6316 (m-10) REVERT: R 178 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7459 (mt-10) outliers start: 27 outliers final: 22 residues processed: 144 average time/residue: 0.1850 time to fit residues: 36.1241 Evaluate side-chains 148 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 78 HIS Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7165 Z= 0.216 Angle : 0.493 7.794 9706 Z= 0.265 Chirality : 0.041 0.139 1125 Planarity : 0.004 0.043 1213 Dihedral : 5.508 57.857 976 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.68 % Allowed : 13.53 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.29), residues: 876 helix: 1.93 (0.26), residues: 414 sheet: -0.34 (0.39), residues: 165 loop : -1.59 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 188 HIS 0.002 0.001 HIS B 91 PHE 0.019 0.002 PHE R 275 TYR 0.009 0.001 TYR B 124 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8364 (ttmt) cc_final: 0.7922 (ttpp) REVERT: A 310 ASP cc_start: 0.7293 (t70) cc_final: 0.7042 (m-30) REVERT: B 75 GLN cc_start: 0.7446 (tt0) cc_final: 0.7222 (tt0) REVERT: B 85 TYR cc_start: 0.7536 (m-80) cc_final: 0.7231 (m-80) REVERT: B 88 ASN cc_start: 0.8420 (m110) cc_final: 0.7851 (m-40) REVERT: B 105 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8564 (t80) REVERT: B 118 ASP cc_start: 0.7947 (p0) cc_final: 0.7034 (t0) REVERT: B 123 ILE cc_start: 0.8844 (mm) cc_final: 0.8639 (mt) REVERT: B 197 ARG cc_start: 0.7507 (mmm160) cc_final: 0.7300 (mmm160) REVERT: R 144 PHE cc_start: 0.6672 (m-80) cc_final: 0.6344 (m-10) REVERT: R 152 VAL cc_start: 0.7884 (t) cc_final: 0.7639 (p) REVERT: R 178 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7472 (mt-10) outliers start: 28 outliers final: 22 residues processed: 145 average time/residue: 0.1803 time to fit residues: 35.5517 Evaluate side-chains 149 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 78 HIS Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7165 Z= 0.216 Angle : 0.492 7.658 9706 Z= 0.264 Chirality : 0.041 0.137 1125 Planarity : 0.004 0.043 1213 Dihedral : 5.449 57.178 976 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.55 % Allowed : 13.53 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.29), residues: 876 helix: 1.88 (0.26), residues: 420 sheet: -0.51 (0.39), residues: 165 loop : -1.57 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 188 HIS 0.003 0.001 HIS B 183 PHE 0.018 0.002 PHE R 275 TYR 0.009 0.001 TYR B 124 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7291 (tp-100) cc_final: 0.7045 (tp-100) REVERT: A 310 ASP cc_start: 0.7299 (t70) cc_final: 0.7043 (m-30) REVERT: B 75 GLN cc_start: 0.7429 (tt0) cc_final: 0.7141 (tt0) REVERT: B 88 ASN cc_start: 0.8382 (m110) cc_final: 0.7802 (m-40) REVERT: B 105 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.8595 (t80) REVERT: B 118 ASP cc_start: 0.7932 (p0) cc_final: 0.7111 (t0) REVERT: B 297 TRP cc_start: 0.8865 (m100) cc_final: 0.8492 (m-10) REVERT: R 144 PHE cc_start: 0.6729 (m-80) cc_final: 0.6396 (m-10) REVERT: R 152 VAL cc_start: 0.7865 (t) cc_final: 0.7622 (p) REVERT: R 178 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7495 (mt-10) outliers start: 27 outliers final: 23 residues processed: 142 average time/residue: 0.1811 time to fit residues: 34.7161 Evaluate side-chains 150 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 78 HIS Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 0.0570 chunk 78 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7165 Z= 0.189 Angle : 0.477 7.594 9706 Z= 0.256 Chirality : 0.040 0.135 1125 Planarity : 0.004 0.043 1213 Dihedral : 5.285 55.666 976 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.29 % Allowed : 13.67 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.29), residues: 876 helix: 1.96 (0.26), residues: 420 sheet: -0.55 (0.39), residues: 167 loop : -1.51 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 188 HIS 0.003 0.001 HIS B 183 PHE 0.018 0.001 PHE R 275 TYR 0.006 0.001 TYR B 124 ARG 0.004 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7713 (ttpp) REVERT: A 310 ASP cc_start: 0.7266 (t70) cc_final: 0.7038 (m-30) REVERT: A 315 LYS cc_start: 0.7828 (mmmt) cc_final: 0.7151 (mmtt) REVERT: B 88 ASN cc_start: 0.8373 (m110) cc_final: 0.7800 (m-40) REVERT: B 105 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8547 (t80) REVERT: B 118 ASP cc_start: 0.7864 (p0) cc_final: 0.7007 (t0) REVERT: B 197 ARG cc_start: 0.7556 (mmm160) cc_final: 0.7350 (tpt90) REVERT: B 297 TRP cc_start: 0.8836 (m100) cc_final: 0.8560 (m-10) REVERT: R 144 PHE cc_start: 0.6713 (m-80) cc_final: 0.6411 (m-10) REVERT: R 152 VAL cc_start: 0.7839 (t) cc_final: 0.7599 (p) REVERT: R 178 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7491 (mt-10) outliers start: 25 outliers final: 21 residues processed: 139 average time/residue: 0.1868 time to fit residues: 34.8819 Evaluate side-chains 149 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 78 HIS Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.151453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122579 restraints weight = 7754.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.123483 restraints weight = 6983.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124577 restraints weight = 6166.468| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7165 Z= 0.203 Angle : 0.490 7.578 9706 Z= 0.262 Chirality : 0.041 0.135 1125 Planarity : 0.004 0.043 1213 Dihedral : 5.260 55.378 976 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.02 % Allowed : 14.06 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.29), residues: 876 helix: 1.98 (0.26), residues: 420 sheet: -0.41 (0.39), residues: 165 loop : -1.53 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 188 HIS 0.002 0.001 HIS B 183 PHE 0.018 0.001 PHE R 275 TYR 0.007 0.001 TYR B 124 ARG 0.003 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1640.32 seconds wall clock time: 30 minutes 43.65 seconds (1843.65 seconds total)