Starting phenix.real_space_refine on Thu Mar 14 08:11:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfz_37209/03_2024/8kfz_37209.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfz_37209/03_2024/8kfz_37209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfz_37209/03_2024/8kfz_37209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfz_37209/03_2024/8kfz_37209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfz_37209/03_2024/8kfz_37209.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfz_37209/03_2024/8kfz_37209.pdb" } resolution = 3.3 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= 0.023 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 66 5.16 5 C 5733 2.51 5 N 1503 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 318": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8966 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2342 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 5, 'TRANS': 282} Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1812 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Time building chain proxies: 5.24, per 1000 atoms: 0.58 Number of scatterers: 8966 At special positions: 0 Unit cell: (87.36, 122.72, 125.84, 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 66 16.00 O 1664 8.00 N 1503 7.00 C 5733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 3.37 Conformation dependent library (CDL) restraints added in 1.7 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 39.2% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'R' and resid 30 through 62 Processing helix chain 'R' and resid 68 through 86 Processing helix chain 'R' and resid 86 through 97 removed outlier: 4.228A pdb=" N PHE R 90 " --> pdb=" O PHE R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 5.113A pdb=" N LYS R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 170 Proline residue: R 167 - end of helix Processing helix chain 'R' and resid 188 through 205 removed outlier: 4.142A pdb=" N LYS R 193 " --> pdb=" O GLN R 189 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TRP R 194 " --> pdb=" O GLN R 190 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN R 203 " --> pdb=" O ASN R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 227 removed outlier: 3.704A pdb=" N ILE R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 250 removed outlier: 3.550A pdb=" N LEU R 248 " --> pdb=" O VAL R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 266 removed outlier: 3.914A pdb=" N ASN R 255 " --> pdb=" O TRP R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 290 Processing helix chain 'R' and resid 291 through 301 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.017A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.944A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.566A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.596A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.819A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.542A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.855A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.566A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 172 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.523A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.882A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.590A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.277A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.984A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.086A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.702A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 5.704A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.258A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.258A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.465A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 135 through 136 removed outlier: 3.591A pdb=" N GLN S 219 " --> pdb=" O THR S 226 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1398 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: 2.81 Time building geometry restraints manager: 3.70 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: 2859 1.34 - 1.46: 2059 1.46 - 1.58: 4140 1.58 - 1.70: 1 1.70 - 1.81: 95 Bond restraints: 9154 Sorted by residual: bond pdb=" N PRO S 169 " pdb=" CD PRO S 169 " ideal model delta sigma weight residual 1.473 1.418 0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" CB PRO S 169 " pdb=" CG PRO S 169 " ideal model delta sigma weight residual 1.492 1.593 -0.101 5.00e-02 4.00e+02 4.11e+00 bond pdb=" CG PRO S 169 " pdb=" CD PRO S 169 " ideal model delta sigma weight residual 1.503 1.552 -0.049 3.40e-02 8.65e+02 2.12e+00 bond pdb=" CB MET S 218 " pdb=" CG MET S 218 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.27e+00 bond pdb=" C VAL A 201 " pdb=" O VAL A 201 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.19e+00 ... (remaining 9149 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.71: 178 106.71 - 113.53: 5042 113.53 - 120.35: 3414 120.35 - 127.17: 3672 127.17 - 133.98: 84 Bond angle restraints: 12390 Sorted by residual: angle pdb=" CA PRO S 169 " pdb=" N PRO S 169 " pdb=" CD PRO S 169 " ideal model delta sigma weight residual 112.00 118.38 -6.38 1.40e+00 5.10e-01 2.08e+01 angle pdb=" C VAL R 85 " pdb=" N PHE R 86 " pdb=" CA PHE R 86 " ideal model delta sigma weight residual 120.28 114.93 5.35 1.44e+00 4.82e-01 1.38e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 128.62 -7.08 1.91e+00 2.74e-01 1.37e+01 angle pdb=" CA LEU R 159 " pdb=" CB LEU R 159 " pdb=" CG LEU R 159 " ideal model delta sigma weight residual 116.30 128.61 -12.31 3.50e+00 8.16e-02 1.24e+01 angle pdb=" N PHE R 86 " pdb=" CA PHE R 86 " pdb=" CB PHE R 86 " ideal model delta sigma weight residual 110.22 115.51 -5.29 1.54e+00 4.22e-01 1.18e+01 ... (remaining 12385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4739 17.90 - 35.81: 526 35.81 - 53.71: 140 53.71 - 71.61: 16 71.61 - 89.52: 2 Dihedral angle restraints: 5423 sinusoidal: 2109 harmonic: 3314 Sorted by residual: dihedral pdb=" CA PHE R 290 " pdb=" C PHE R 290 " pdb=" N THR R 291 " pdb=" CA THR R 291 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA MET R 266 " pdb=" C MET R 266 " pdb=" N HIS R 267 " pdb=" CA HIS R 267 " ideal model delta harmonic sigma weight residual 180.00 155.48 24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASN S 159 " pdb=" C ASN S 159 " pdb=" N THR S 160 " pdb=" CA THR S 160 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1270 0.072 - 0.145: 135 0.145 - 0.217: 8 0.217 - 0.290: 0 0.290 - 0.362: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CB ILE R 115 " pdb=" CA ILE R 115 " pdb=" CG1 ILE R 115 " pdb=" CG2 ILE R 115 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CG LEU A 268 " pdb=" CB LEU A 268 " pdb=" CD1 LEU A 268 " pdb=" CD2 LEU A 268 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL A 339 " pdb=" CA VAL A 339 " pdb=" CG1 VAL A 339 " pdb=" CG2 VAL A 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 1411 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 251 " -0.026 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP R 251 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP R 251 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP R 251 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 251 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 251 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 251 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 251 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 251 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP R 251 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 86 " 0.029 2.00e-02 2.50e+03 2.46e-02 1.05e+01 pdb=" CG PHE R 86 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE R 86 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE R 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE R 86 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE R 86 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE R 86 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.57e+00 pdb=" N PRO C 49 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.029 5.00e-02 4.00e+02 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1029 2.75 - 3.28: 9143 3.28 - 3.82: 15574 3.82 - 4.36: 18629 4.36 - 4.90: 31446 Nonbonded interactions: 75821 Sorted by model distance: nonbonded pdb=" O SER S 85 " pdb=" NH1 ARG S 87 " model vdw 2.206 2.520 nonbonded pdb=" ND1 HIS B 311 " pdb=" OG SER B 331 " model vdw 2.233 2.520 nonbonded pdb=" O LYS R 306 " pdb=" ND1 HIS R 310 " model vdw 2.257 2.520 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.258 2.440 nonbonded pdb=" O PHE R 88 " pdb=" OG1 THR R 92 " model vdw 2.259 2.440 ... (remaining 75816 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 3.780 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.270 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 9154 Z= 0.228 Angle : 0.667 12.307 12390 Z= 0.356 Chirality : 0.045 0.362 1414 Planarity : 0.004 0.053 1554 Dihedral : 15.611 89.516 3276 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.10 % Allowed : 28.85 % Favored : 71.05 % 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: 0.79 (0.25), residues: 1125 helix: 1.73 (0.26), residues: 399 sheet: 0.05 (0.29), residues: 284 loop : -0.16 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP R 251 HIS 0.004 0.001 HIS S 155 PHE 0.056 0.002 PHE R 86 TYR 0.022 0.002 TYR S 178 ARG 0.008 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 303 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 121 MET cc_start: 0.7320 (mmt) cc_final: 0.7027 (mmt) REVERT: R 131 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7923 (mtt180) REVERT: R 132 TYR cc_start: 0.8680 (t80) cc_final: 0.8449 (t80) REVERT: B 57 LYS cc_start: 0.7624 (mtmt) cc_final: 0.7149 (mtmt) REVERT: B 130 GLU cc_start: 0.7745 (mp0) cc_final: 0.7297 (mp0) REVERT: B 169 TRP cc_start: 0.7798 (m100) cc_final: 0.7593 (m100) REVERT: S 38 ARG cc_start: 0.7426 (ptt180) cc_final: 0.7031 (ptt180) REVERT: S 90 ASP cc_start: 0.7234 (m-30) cc_final: 0.6980 (m-30) REVERT: S 167 GLN cc_start: 0.8221 (tt0) cc_final: 0.7951 (tp40) outliers start: 1 outliers final: 1 residues processed: 304 average time/residue: 0.2528 time to fit residues: 18503.0813 Evaluate side-chains 292 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 291 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 183 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.0000 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN B 132 ASN B 155 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9154 Z= 0.219 Angle : 0.594 8.110 12390 Z= 0.316 Chirality : 0.043 0.221 1414 Planarity : 0.004 0.052 1554 Dihedral : 4.714 27.513 1227 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.15 % Allowed : 25.20 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1125 helix: 1.90 (0.26), residues: 400 sheet: 0.21 (0.29), residues: 286 loop : -0.23 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 251 HIS 0.003 0.001 HIS A 244 PHE 0.042 0.002 PHE R 86 TYR 0.018 0.002 TYR R 118 ARG 0.006 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 300 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 PHE cc_start: 0.7013 (m-80) cc_final: 0.6664 (m-80) REVERT: R 121 MET cc_start: 0.7647 (mmt) cc_final: 0.6903 (mmt) REVERT: R 220 LYS cc_start: 0.8588 (mmmm) cc_final: 0.8174 (mmmm) REVERT: A 197 LYS cc_start: 0.7479 (mtmt) cc_final: 0.7051 (mtmt) REVERT: A 243 MET cc_start: 0.8373 (mmm) cc_final: 0.7771 (tpp) REVERT: A 349 LYS cc_start: 0.7855 (mtmt) cc_final: 0.7490 (ttmt) REVERT: B 57 LYS cc_start: 0.7671 (mtmt) cc_final: 0.7177 (mtmt) REVERT: B 130 GLU cc_start: 0.7743 (mp0) cc_final: 0.7239 (mp0) REVERT: B 169 TRP cc_start: 0.7825 (m100) cc_final: 0.7620 (m100) REVERT: B 183 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7007 (t-170) REVERT: S 18 ARG cc_start: 0.7104 (tmm-80) cc_final: 0.6902 (tmm-80) REVERT: S 38 ARG cc_start: 0.7171 (ptt180) cc_final: 0.6758 (ptt180) REVERT: S 90 ASP cc_start: 0.7275 (m-30) cc_final: 0.6995 (m-30) outliers start: 41 outliers final: 30 residues processed: 317 average time/residue: 0.2340 time to fit residues: 98.0450 Evaluate side-chains 328 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 297 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.0770 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 GLN B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9154 Z= 0.205 Angle : 0.571 11.187 12390 Z= 0.302 Chirality : 0.042 0.238 1414 Planarity : 0.004 0.048 1554 Dihedral : 4.675 28.122 1227 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.35 % Allowed : 24.90 % Favored : 70.75 % 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: 0.96 (0.25), residues: 1125 helix: 1.94 (0.26), residues: 407 sheet: 0.17 (0.29), residues: 286 loop : -0.22 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 251 HIS 0.003 0.001 HIS A 244 PHE 0.031 0.002 PHE R 86 TYR 0.015 0.001 TYR B 289 ARG 0.004 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 296 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 PHE cc_start: 0.7130 (m-80) cc_final: 0.6696 (m-80) REVERT: R 121 MET cc_start: 0.7587 (mmt) cc_final: 0.6912 (mmt) REVERT: A 197 LYS cc_start: 0.7452 (mtmt) cc_final: 0.7086 (mtmt) REVERT: A 200 ASP cc_start: 0.7560 (t0) cc_final: 0.7274 (t0) REVERT: A 243 MET cc_start: 0.8388 (mmm) cc_final: 0.7731 (tpp) REVERT: A 332 VAL cc_start: 0.8065 (m) cc_final: 0.7817 (p) REVERT: A 345 LYS cc_start: 0.7863 (tttm) cc_final: 0.7651 (tttm) REVERT: A 349 LYS cc_start: 0.7852 (mtmt) cc_final: 0.7479 (ttmt) REVERT: B 130 GLU cc_start: 0.7815 (mp0) cc_final: 0.7280 (mp0) REVERT: B 169 TRP cc_start: 0.7828 (m100) cc_final: 0.7624 (m100) REVERT: B 183 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.6995 (t-170) REVERT: S 38 ARG cc_start: 0.7130 (ptt180) cc_final: 0.6724 (ptt180) REVERT: S 90 ASP cc_start: 0.7286 (m-30) cc_final: 0.7005 (m-30) REVERT: S 171 GLN cc_start: 0.6679 (mm-40) cc_final: 0.6344 (tm-30) outliers start: 43 outliers final: 35 residues processed: 315 average time/residue: 0.2379 time to fit residues: 98.3618 Evaluate side-chains 327 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 291 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 189 ASP Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.0050 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 60 optimal weight: 0.0570 overall best weight: 0.4512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 76 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9154 Z= 0.168 Angle : 0.548 11.068 12390 Z= 0.288 Chirality : 0.042 0.271 1414 Planarity : 0.004 0.050 1554 Dihedral : 4.519 28.791 1227 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.35 % Allowed : 26.11 % Favored : 69.53 % 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: 1.10 (0.25), residues: 1125 helix: 2.16 (0.26), residues: 399 sheet: 0.24 (0.30), residues: 282 loop : -0.19 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 251 HIS 0.004 0.001 HIS A 244 PHE 0.021 0.001 PHE R 86 TYR 0.013 0.001 TYR B 289 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 288 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 PHE cc_start: 0.7242 (m-80) cc_final: 0.6774 (m-80) REVERT: R 121 MET cc_start: 0.7598 (mmt) cc_final: 0.7038 (mmt) REVERT: R 159 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6949 (mp) REVERT: R 220 LYS cc_start: 0.8520 (mmmm) cc_final: 0.8078 (mmmm) REVERT: R 237 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7673 (tt) REVERT: A 197 LYS cc_start: 0.7426 (mtmt) cc_final: 0.7041 (mtmt) REVERT: A 200 ASP cc_start: 0.7534 (t0) cc_final: 0.7238 (t0) REVERT: A 243 MET cc_start: 0.8412 (mmm) cc_final: 0.7726 (tpp) REVERT: A 277 LYS cc_start: 0.6972 (tmtt) cc_final: 0.6413 (ptmt) REVERT: A 332 VAL cc_start: 0.8055 (m) cc_final: 0.7814 (p) REVERT: A 349 LYS cc_start: 0.7863 (mtmt) cc_final: 0.7552 (ttmt) REVERT: B 19 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8145 (ttp80) REVERT: B 49 ARG cc_start: 0.8340 (mmt-90) cc_final: 0.7919 (mpt180) REVERT: B 52 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7110 (mmm-85) REVERT: B 111 TYR cc_start: 0.8043 (m-80) cc_final: 0.7813 (m-80) REVERT: B 130 GLU cc_start: 0.7779 (mp0) cc_final: 0.7220 (mp0) REVERT: B 183 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.6980 (t-170) REVERT: B 283 ARG cc_start: 0.7854 (mmm-85) cc_final: 0.7453 (tpt170) REVERT: B 289 TYR cc_start: 0.8167 (m-80) cc_final: 0.7715 (m-80) REVERT: S 38 ARG cc_start: 0.7094 (ptt180) cc_final: 0.6657 (ptt180) REVERT: S 90 ASP cc_start: 0.7279 (m-30) cc_final: 0.7002 (m-30) REVERT: S 171 GLN cc_start: 0.6683 (mm-40) cc_final: 0.6344 (tm-30) REVERT: S 227 PHE cc_start: 0.6927 (m-80) cc_final: 0.6490 (m-80) outliers start: 43 outliers final: 28 residues processed: 308 average time/residue: 0.2345 time to fit residues: 95.2040 Evaluate side-chains 315 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 283 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 189 ASP Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.0970 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 HIS ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9154 Z= 0.249 Angle : 0.588 12.615 12390 Z= 0.309 Chirality : 0.043 0.205 1414 Planarity : 0.004 0.061 1554 Dihedral : 4.625 28.986 1227 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.87 % Allowed : 24.70 % Favored : 69.43 % 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: 0.99 (0.25), residues: 1125 helix: 2.06 (0.26), residues: 404 sheet: 0.14 (0.29), residues: 284 loop : -0.25 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 251 HIS 0.004 0.001 HIS R 231 PHE 0.021 0.002 PHE A 336 TYR 0.015 0.002 TYR R 300 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 292 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 PHE cc_start: 0.7336 (m-80) cc_final: 0.6887 (m-80) REVERT: R 118 TYR cc_start: 0.6324 (m-80) cc_final: 0.5990 (m-80) REVERT: R 121 MET cc_start: 0.7625 (mmt) cc_final: 0.6945 (mmt) REVERT: R 149 MET cc_start: 0.6871 (tpt) cc_final: 0.6304 (tpt) REVERT: R 152 THR cc_start: 0.7242 (m) cc_final: 0.6935 (t) REVERT: R 159 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6982 (mp) REVERT: R 211 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: R 220 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8153 (mmmm) REVERT: R 237 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7707 (tt) REVERT: R 285 THR cc_start: 0.7468 (t) cc_final: 0.7206 (p) REVERT: A 197 LYS cc_start: 0.7485 (mtmt) cc_final: 0.7042 (mtmt) REVERT: A 277 LYS cc_start: 0.7140 (tmtt) cc_final: 0.6540 (ptmt) REVERT: A 321 THR cc_start: 0.8393 (m) cc_final: 0.8067 (t) REVERT: A 332 VAL cc_start: 0.8059 (m) cc_final: 0.7790 (p) REVERT: A 349 LYS cc_start: 0.7852 (mtmt) cc_final: 0.7584 (ttmt) REVERT: B 19 ARG cc_start: 0.8402 (ttp80) cc_final: 0.8160 (ttp80) REVERT: B 49 ARG cc_start: 0.8369 (mmt-90) cc_final: 0.7975 (mpt180) REVERT: B 130 GLU cc_start: 0.7780 (mp0) cc_final: 0.7175 (mp0) REVERT: B 183 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7087 (t-170) REVERT: S 38 ARG cc_start: 0.7267 (ptt180) cc_final: 0.6893 (ptt180) REVERT: S 87 ARG cc_start: 0.7568 (ptp90) cc_final: 0.7306 (ptp90) REVERT: S 90 ASP cc_start: 0.7275 (m-30) cc_final: 0.7020 (m-30) REVERT: S 171 GLN cc_start: 0.6687 (mm-40) cc_final: 0.6371 (tm-30) outliers start: 58 outliers final: 41 residues processed: 321 average time/residue: 0.2311 time to fit residues: 98.2538 Evaluate side-chains 340 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 295 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 189 ASP Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 211 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN B 132 ASN B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9154 Z= 0.213 Angle : 0.583 13.168 12390 Z= 0.303 Chirality : 0.043 0.303 1414 Planarity : 0.004 0.062 1554 Dihedral : 4.618 29.404 1227 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.77 % Allowed : 25.71 % Favored : 68.52 % 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: 0.99 (0.25), residues: 1125 helix: 2.06 (0.26), residues: 404 sheet: 0.13 (0.29), residues: 285 loop : -0.24 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 251 HIS 0.003 0.001 HIS S 35 PHE 0.022 0.002 PHE A 336 TYR 0.020 0.001 TYR R 300 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 294 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 PHE cc_start: 0.7348 (m-80) cc_final: 0.6965 (m-80) REVERT: R 121 MET cc_start: 0.7597 (mmt) cc_final: 0.6916 (mmt) REVERT: R 149 MET cc_start: 0.6853 (tpt) cc_final: 0.6353 (tpt) REVERT: R 152 THR cc_start: 0.7217 (m) cc_final: 0.6914 (t) REVERT: R 159 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6990 (mp) REVERT: R 211 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7059 (m-80) REVERT: R 237 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7681 (tt) REVERT: R 285 THR cc_start: 0.7375 (t) cc_final: 0.7144 (p) REVERT: R 306 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7129 (pttm) REVERT: A 197 LYS cc_start: 0.7481 (mtmt) cc_final: 0.7034 (mtmt) REVERT: A 277 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6560 (ptmt) REVERT: A 321 THR cc_start: 0.8373 (m) cc_final: 0.8046 (t) REVERT: A 332 VAL cc_start: 0.8058 (m) cc_final: 0.7773 (p) REVERT: A 349 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7573 (ttmt) REVERT: B 19 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8144 (ttp80) REVERT: B 29 THR cc_start: 0.8034 (t) cc_final: 0.7539 (p) REVERT: B 49 ARG cc_start: 0.8330 (mmt-90) cc_final: 0.7941 (mpt180) REVERT: B 52 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7101 (mmm-85) REVERT: B 130 GLU cc_start: 0.7744 (mp0) cc_final: 0.7118 (mp0) REVERT: B 183 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7063 (t-170) REVERT: S 38 ARG cc_start: 0.7259 (ptt180) cc_final: 0.6915 (ptt180) REVERT: S 90 ASP cc_start: 0.7286 (m-30) cc_final: 0.7017 (m-30) REVERT: S 116 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7464 (p) REVERT: S 171 GLN cc_start: 0.6691 (mm-40) cc_final: 0.6373 (tm-30) outliers start: 57 outliers final: 39 residues processed: 323 average time/residue: 0.2267 time to fit residues: 97.2669 Evaluate side-chains 341 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 294 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 189 ASP Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 211 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9154 Z= 0.229 Angle : 0.596 13.485 12390 Z= 0.311 Chirality : 0.044 0.320 1414 Planarity : 0.004 0.062 1554 Dihedral : 4.655 29.444 1227 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.57 % Allowed : 26.82 % Favored : 67.61 % 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: 0.90 (0.25), residues: 1125 helix: 2.04 (0.26), residues: 399 sheet: 0.08 (0.29), residues: 285 loop : -0.31 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 251 HIS 0.003 0.001 HIS S 155 PHE 0.035 0.002 PHE R 88 TYR 0.022 0.001 TYR R 300 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 290 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 PHE cc_start: 0.7237 (m-80) cc_final: 0.6823 (m-80) REVERT: R 121 MET cc_start: 0.7626 (mmt) cc_final: 0.6938 (mmt) REVERT: R 152 THR cc_start: 0.7269 (m) cc_final: 0.7060 (t) REVERT: R 159 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6996 (mp) REVERT: R 211 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: R 220 LYS cc_start: 0.8564 (mmmm) cc_final: 0.8129 (mmmm) REVERT: R 285 THR cc_start: 0.7351 (t) cc_final: 0.7104 (p) REVERT: R 306 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7136 (pttm) REVERT: A 197 LYS cc_start: 0.7558 (mtmt) cc_final: 0.7095 (mtmt) REVERT: A 277 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6592 (ptmt) REVERT: A 321 THR cc_start: 0.8403 (m) cc_final: 0.8081 (t) REVERT: A 332 VAL cc_start: 0.8071 (m) cc_final: 0.7779 (p) REVERT: A 349 LYS cc_start: 0.7842 (mtmt) cc_final: 0.7523 (ttmt) REVERT: B 19 ARG cc_start: 0.8377 (ttp80) cc_final: 0.8116 (ttp80) REVERT: B 29 THR cc_start: 0.8040 (t) cc_final: 0.7547 (p) REVERT: B 49 ARG cc_start: 0.8337 (mmt-90) cc_final: 0.7956 (mpt180) REVERT: B 52 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7098 (mmm-85) REVERT: B 130 GLU cc_start: 0.7760 (mp0) cc_final: 0.7180 (mp0) REVERT: B 183 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7095 (t-170) REVERT: B 289 TYR cc_start: 0.8211 (m-80) cc_final: 0.7716 (m-80) REVERT: S 38 ARG cc_start: 0.7337 (ptt180) cc_final: 0.7040 (ptt180) REVERT: S 90 ASP cc_start: 0.7211 (m-30) cc_final: 0.6942 (m-30) REVERT: S 116 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7481 (p) REVERT: S 171 GLN cc_start: 0.6714 (mm-40) cc_final: 0.6409 (tm-30) outliers start: 55 outliers final: 40 residues processed: 316 average time/residue: 0.2426 time to fit residues: 101.3017 Evaluate side-chains 337 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 290 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 189 ASP Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 211 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9154 Z= 0.256 Angle : 0.618 14.021 12390 Z= 0.320 Chirality : 0.044 0.331 1414 Planarity : 0.004 0.061 1554 Dihedral : 4.705 29.564 1227 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.47 % Allowed : 26.92 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1125 helix: 1.86 (0.26), residues: 405 sheet: 0.00 (0.29), residues: 285 loop : -0.32 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 251 HIS 0.003 0.001 HIS S 155 PHE 0.028 0.002 PHE A 336 TYR 0.021 0.002 TYR R 300 ARG 0.006 0.001 ARG S 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 299 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 PHE cc_start: 0.7367 (m-80) cc_final: 0.6923 (m-80) REVERT: R 121 MET cc_start: 0.7609 (mmt) cc_final: 0.7016 (mmt) REVERT: R 159 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7002 (mp) REVERT: R 211 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7016 (m-80) REVERT: R 220 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8086 (mmmm) REVERT: R 249 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6466 (mm) REVERT: R 285 THR cc_start: 0.7363 (t) cc_final: 0.7120 (p) REVERT: R 306 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7153 (pttm) REVERT: A 197 LYS cc_start: 0.7591 (mtmt) cc_final: 0.7123 (mtmt) REVERT: A 270 LYS cc_start: 0.8071 (mmtm) cc_final: 0.7816 (mmtm) REVERT: A 277 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6665 (ptmt) REVERT: A 321 THR cc_start: 0.8448 (m) cc_final: 0.8143 (t) REVERT: A 332 VAL cc_start: 0.8065 (m) cc_final: 0.7759 (p) REVERT: A 349 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7582 (ttmt) REVERT: B 29 THR cc_start: 0.8047 (t) cc_final: 0.7539 (p) REVERT: B 49 ARG cc_start: 0.8327 (mmt-90) cc_final: 0.7931 (mpt180) REVERT: B 52 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7104 (mmm-85) REVERT: B 130 GLU cc_start: 0.7769 (mp0) cc_final: 0.7195 (mp0) REVERT: B 169 TRP cc_start: 0.7924 (m100) cc_final: 0.7644 (m100) REVERT: B 183 HIS cc_start: 0.8151 (OUTLIER) cc_final: 0.7162 (t-170) REVERT: B 314 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7081 (ttm-80) REVERT: S 38 ARG cc_start: 0.7451 (ptt180) cc_final: 0.7160 (ptt180) REVERT: S 90 ASP cc_start: 0.7204 (m-30) cc_final: 0.6926 (m-30) REVERT: S 106 SER cc_start: 0.8090 (t) cc_final: 0.7879 (t) REVERT: S 116 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7499 (p) REVERT: S 171 GLN cc_start: 0.6733 (mm-40) cc_final: 0.6430 (tm-30) outliers start: 54 outliers final: 38 residues processed: 325 average time/residue: 0.2332 time to fit residues: 99.7233 Evaluate side-chains 344 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 297 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 189 ASP Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 211 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 0.2980 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9154 Z= 0.212 Angle : 0.612 13.873 12390 Z= 0.316 Chirality : 0.044 0.331 1414 Planarity : 0.004 0.059 1554 Dihedral : 4.645 29.631 1227 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.86 % Allowed : 27.63 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1125 helix: 1.88 (0.26), residues: 405 sheet: 0.02 (0.29), residues: 288 loop : -0.28 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP R 251 HIS 0.003 0.001 HIS S 155 PHE 0.027 0.002 PHE A 336 TYR 0.018 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 291 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 PHE cc_start: 0.7328 (m-80) cc_final: 0.6903 (m-80) REVERT: R 118 TYR cc_start: 0.6474 (m-80) cc_final: 0.6210 (m-80) REVERT: R 121 MET cc_start: 0.7617 (mmt) cc_final: 0.6932 (mmt) REVERT: R 159 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7006 (mp) REVERT: R 211 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.6921 (m-80) REVERT: R 220 LYS cc_start: 0.8581 (mmmm) cc_final: 0.8117 (mmmm) REVERT: R 249 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6430 (mm) REVERT: R 306 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6992 (tttt) REVERT: A 197 LYS cc_start: 0.7590 (mtmt) cc_final: 0.7137 (mtmt) REVERT: A 270 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7800 (mmtm) REVERT: A 277 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6796 (ptmt) REVERT: A 321 THR cc_start: 0.8407 (m) cc_final: 0.8094 (t) REVERT: A 332 VAL cc_start: 0.8075 (m) cc_final: 0.7755 (p) REVERT: A 349 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7589 (ttmt) REVERT: B 29 THR cc_start: 0.8016 (t) cc_final: 0.7536 (p) REVERT: B 49 ARG cc_start: 0.8300 (mmt-90) cc_final: 0.7928 (mpt180) REVERT: B 52 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7094 (mmm-85) REVERT: B 75 GLN cc_start: 0.8388 (mm110) cc_final: 0.8009 (mm110) REVERT: B 130 GLU cc_start: 0.7773 (mp0) cc_final: 0.7181 (mp0) REVERT: B 169 TRP cc_start: 0.7866 (m100) cc_final: 0.7582 (m100) REVERT: B 183 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7154 (t-170) REVERT: B 289 TYR cc_start: 0.8176 (m-80) cc_final: 0.7685 (m-80) REVERT: S 38 ARG cc_start: 0.7349 (ptt180) cc_final: 0.7066 (ptt180) REVERT: S 90 ASP cc_start: 0.7212 (m-30) cc_final: 0.6999 (m-30) REVERT: S 116 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7492 (p) REVERT: S 171 GLN cc_start: 0.6735 (mm-40) cc_final: 0.6437 (tm-30) outliers start: 48 outliers final: 36 residues processed: 313 average time/residue: 0.2369 time to fit residues: 98.4455 Evaluate side-chains 333 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 289 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 189 ASP Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 211 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 93 optimal weight: 0.0370 chunk 26 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9154 Z= 0.194 Angle : 0.607 14.447 12390 Z= 0.312 Chirality : 0.044 0.324 1414 Planarity : 0.004 0.055 1554 Dihedral : 4.600 29.853 1227 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.55 % Allowed : 27.63 % Favored : 67.81 % 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: 0.90 (0.26), residues: 1125 helix: 2.00 (0.26), residues: 399 sheet: 0.05 (0.29), residues: 290 loop : -0.26 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP R 251 HIS 0.003 0.001 HIS S 35 PHE 0.027 0.002 PHE A 336 TYR 0.016 0.001 TYR R 300 ARG 0.004 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 280 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 86 PHE cc_start: 0.7310 (m-80) cc_final: 0.6910 (m-80) REVERT: R 118 TYR cc_start: 0.6483 (m-80) cc_final: 0.6237 (m-80) REVERT: R 121 MET cc_start: 0.7620 (mmt) cc_final: 0.6944 (mmt) REVERT: R 149 MET cc_start: 0.6724 (tpt) cc_final: 0.6313 (tpt) REVERT: R 159 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7006 (mp) REVERT: R 211 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: R 220 LYS cc_start: 0.8579 (mmmm) cc_final: 0.8139 (mmmm) REVERT: R 306 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6997 (tttt) REVERT: A 197 LYS cc_start: 0.7585 (mtmt) cc_final: 0.7152 (mtmt) REVERT: A 270 LYS cc_start: 0.8034 (mmtm) cc_final: 0.7755 (mmtm) REVERT: A 277 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6842 (ptmt) REVERT: A 321 THR cc_start: 0.8397 (m) cc_final: 0.8092 (t) REVERT: A 332 VAL cc_start: 0.8087 (m) cc_final: 0.7756 (p) REVERT: A 337 ASP cc_start: 0.7433 (m-30) cc_final: 0.7164 (m-30) REVERT: A 349 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7523 (ttmt) REVERT: B 29 THR cc_start: 0.8010 (t) cc_final: 0.7496 (p) REVERT: B 49 ARG cc_start: 0.8273 (mmt-90) cc_final: 0.7899 (mpt180) REVERT: B 52 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7092 (mmm-85) REVERT: B 75 GLN cc_start: 0.8349 (mm110) cc_final: 0.7995 (mm110) REVERT: B 130 GLU cc_start: 0.7707 (mp0) cc_final: 0.7111 (mp0) REVERT: B 169 TRP cc_start: 0.7823 (m100) cc_final: 0.7499 (m100) REVERT: B 183 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7185 (t-170) REVERT: B 283 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7435 (tpt170) REVERT: B 289 TYR cc_start: 0.8162 (m-80) cc_final: 0.7682 (m-80) REVERT: S 38 ARG cc_start: 0.7329 (ptt180) cc_final: 0.6979 (ptt180) REVERT: S 87 ARG cc_start: 0.7587 (ptp90) cc_final: 0.7370 (ptp90) REVERT: S 171 GLN cc_start: 0.6745 (mm-40) cc_final: 0.6454 (tm-30) outliers start: 45 outliers final: 37 residues processed: 302 average time/residue: 0.2299 time to fit residues: 91.7075 Evaluate side-chains 322 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 279 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 211 PHE Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 292 HIS Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 189 ASP Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 211 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 36 optimal weight: 0.0170 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.157228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.128788 restraints weight = 15183.453| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.68 r_work: 0.3512 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 9154 Z= 0.271 Angle : 0.913 59.173 12390 Z= 0.526 Chirality : 0.045 0.454 1414 Planarity : 0.004 0.063 1554 Dihedral : 4.710 34.558 1227 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.55 % Allowed : 28.04 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.87 (0.25), residues: 1125 helix: 2.00 (0.26), residues: 399 sheet: 0.05 (0.29), residues: 290 loop : -0.30 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 251 HIS 0.003 0.001 HIS S 35 PHE 0.029 0.002 PHE S 227 TYR 0.016 0.001 TYR R 300 ARG 0.009 0.000 ARG S 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2658.44 seconds wall clock time: 355 minutes 0.19 seconds (21300.19 seconds total)