Starting phenix.real_space_refine on Wed Mar 4 13:23:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s0g_24790/03_2026/7s0g_24790_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s0g_24790/03_2026/7s0g_24790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s0g_24790/03_2026/7s0g_24790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s0g_24790/03_2026/7s0g_24790.map" model { file = "/net/cci-nas-00/data/ceres_data/7s0g_24790/03_2026/7s0g_24790_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s0g_24790/03_2026/7s0g_24790_trim.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.968 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: 5 Type Number sf(0) Gaussians S 51 5.16 5 C 4451 2.51 5 N 1198 2.21 5 O 1292 1.98 5 H 6854 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13846 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 4248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4248 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5098 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3526 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 959 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'5FW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.16, per 1000 atoms: 0.16 Number of scatterers: 13846 At special positions: 0 Unit cell: (84.8065, 98.762, 130.967, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 O 1292 8.00 N 1198 7.00 C 4451 6.00 H 6854 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 199 " distance=2.03 Simple disulfide: pdb=" SG CYS R 192 " - pdb=" SG CYS R 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 373.3 milliseconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 47.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'R' and resid 40 through 69 removed outlier: 3.915A pdb=" N LEU R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU R 47 " --> pdb=" O GLY R 43 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR R 69 " --> pdb=" O ALA R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 105 removed outlier: 3.591A pdb=" N LEU R 78 " --> pdb=" O THR R 74 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) Proline residue: R 96 - end of helix Processing helix chain 'R' and resid 110 through 145 Processing helix chain 'R' and resid 145 through 153 Processing helix chain 'R' and resid 154 through 179 removed outlier: 4.186A pdb=" N LEU R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Proline residue: R 176 - end of helix Processing helix chain 'R' and resid 186 through 195 Processing helix chain 'R' and resid 204 through 216 removed outlier: 3.745A pdb=" N ALA R 208 " --> pdb=" O ASN R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 241 Processing helix chain 'R' and resid 286 through 316 removed outlier: 3.672A pdb=" N ILE R 295 " --> pdb=" O THR R 291 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Proline residue: R 305 - end of helix removed outlier: 3.584A pdb=" N VAL R 314 " --> pdb=" O ASN R 310 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE R 315 " --> pdb=" O ILE R 311 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN R 316 " --> pdb=" O VAL R 312 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 320 removed outlier: 3.665A pdb=" N VAL R 320 " --> pdb=" O ARG R 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 317 through 320' Processing helix chain 'R' and resid 321 through 344 removed outlier: 3.747A pdb=" N PHE R 325 " --> pdb=" O PRO R 321 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER R 336 " --> pdb=" O GLY R 332 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA R 337 " --> pdb=" O TYR R 333 " (cutoff:3.500A) Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 346 through 356 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.612A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.562A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.598A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.677A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.552A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.098A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.101A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.659A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 150 removed outlier: 7.013A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 190 through 192 removed outlier: 6.663A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.611A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.746A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191 removed outlier: 7.827A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.24 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6828 1.03 - 1.23: 36 1.23 - 1.43: 2999 1.43 - 1.62: 4051 1.62 - 1.82: 72 Bond restraints: 13986 Sorted by residual: bond pdb=" CAM 5FW R 401 " pdb=" OAB 5FW R 401 " ideal model delta sigma weight residual 1.353 1.438 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" CAO 5FW R 401 " pdb=" OAC 5FW R 401 " ideal model delta sigma weight residual 1.351 1.417 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 1.457 1.493 -0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" CAE 5FW R 401 " pdb=" CAH 5FW R 401 " ideal model delta sigma weight residual 1.515 1.546 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" CAG 5FW R 401 " pdb=" CAJ 5FW R 401 " ideal model delta sigma weight residual 1.530 1.501 0.029 2.00e-02 2.50e+03 2.16e+00 ... (remaining 13981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.99: 25180 21.99 - 43.98: 0 43.98 - 65.97: 0 65.97 - 87.96: 0 87.96 - 109.94: 1 Bond angle restraints: 25181 Sorted by residual: angle pdb=" HB2 GLU A 352 " pdb=" CB GLU A 352 " pdb=" HB3 GLU A 352 " ideal model delta sigma weight residual 110.00 0.06 109.94 3.00e+00 1.11e-01 1.34e+03 angle pdb=" C VAL R 95 " pdb=" CA VAL R 95 " pdb=" CB VAL R 95 " ideal model delta sigma weight residual 114.00 110.72 3.28 1.31e+00 5.83e-01 6.28e+00 angle pdb=" N VAL A 201 " pdb=" CA VAL A 201 " pdb=" C VAL A 201 " ideal model delta sigma weight residual 111.88 109.50 2.38 1.06e+00 8.90e-01 5.03e+00 angle pdb=" C VAL R 94 " pdb=" N VAL R 95 " pdb=" CA VAL R 95 " ideal model delta sigma weight residual 120.33 122.02 -1.69 8.00e-01 1.56e+00 4.44e+00 angle pdb=" CAJ 5FW R 401 " pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 114.52 109.00 5.52 3.00e+00 1.11e-01 3.39e+00 ... (remaining 25176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.60: 5984 15.60 - 31.20: 449 31.20 - 46.81: 97 46.81 - 62.41: 50 62.41 - 78.01: 7 Dihedral angle restraints: 6587 sinusoidal: 3491 harmonic: 3096 Sorted by residual: dihedral pdb=" CA ASP B 153 " pdb=" CB ASP B 153 " pdb=" CG ASP B 153 " pdb=" OD1 ASP B 153 " ideal model delta sinusoidal sigma weight residual -30.00 -82.44 52.44 1 2.00e+01 2.50e-03 9.37e+00 dihedral pdb=" CA ASP B 312 " pdb=" CB ASP B 312 " pdb=" CG ASP B 312 " pdb=" OD1 ASP B 312 " ideal model delta sinusoidal sigma weight residual -30.00 -82.17 52.17 1 2.00e+01 2.50e-03 9.28e+00 dihedral pdb=" CA ASN R 310 " pdb=" CB ASN R 310 " pdb=" CG ASN R 310 " pdb=" OD1 ASN R 310 " ideal model delta sinusoidal sigma weight residual 120.00 178.63 -58.63 2 2.00e+01 2.50e-03 8.75e+00 ... (remaining 6584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 984 0.057 - 0.114: 111 0.114 - 0.171: 11 0.171 - 0.229: 0 0.229 - 0.286: 1 Chirality restraints: 1107 Sorted by residual: chirality pdb=" CAE 5FW R 401 " pdb=" CAF 5FW R 401 " pdb=" CAH 5FW R 401 " pdb=" OAA 5FW R 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.58 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1104 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.38e+00 pdb=" N PRO G 49 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 218 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO R 219 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO R 219 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 219 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 320 " -0.016 5.00e-02 4.00e+02 2.39e-02 9.13e-01 pdb=" N PRO R 321 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO R 321 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 321 " -0.013 5.00e-02 4.00e+02 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1067 2.23 - 2.82: 30218 2.82 - 3.41: 35336 3.41 - 4.01: 47215 4.01 - 4.60: 73202 Nonbonded interactions: 187038 Sorted by model distance: nonbonded pdb=" HG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 1.635 2.450 nonbonded pdb=" OE1 GLU A 289 " pdb=" H GLU A 289 " model vdw 1.641 2.450 nonbonded pdb=" OD1 ASP B 205 " pdb=" HG SER B 207 " model vdw 1.668 2.450 nonbonded pdb=" OD1 ASP R 184 " pdb=" H ASP R 186 " model vdw 1.681 2.450 nonbonded pdb="HH11 ARG B 251 " pdb=" OE2 GLU B 260 " model vdw 1.686 2.450 ... (remaining 187033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.050 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 7134 Z= 0.143 Angle : 0.441 5.523 9673 Z= 0.261 Chirality : 0.037 0.286 1107 Planarity : 0.002 0.029 1224 Dihedral : 12.412 78.012 2543 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.27), residues: 881 helix: 0.26 (0.24), residues: 403 sheet: -2.74 (0.35), residues: 158 loop : -2.36 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 229 TYR 0.008 0.001 TYR G 40 PHE 0.009 0.001 PHE R 174 TRP 0.005 0.001 TRP R 117 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7132) covalent geometry : angle 0.44098 ( 9669) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.60446 ( 4) hydrogen bonds : bond 0.09844 ( 378) hydrogen bonds : angle 4.43579 ( 1095) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 322 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.260 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: symmetry clash 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 116 LEU cc_start: 0.8061 (tt) cc_final: 0.7857 (tt) REVERT: R 236 GLU cc_start: 0.8452 (tt0) cc_final: 0.8201 (tt0) REVERT: R 240 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8394 (mttt) REVERT: R 285 GLU cc_start: 0.7637 (pm20) cc_final: 0.7348 (mt-10) REVERT: R 323 TRP cc_start: 0.7904 (p-90) cc_final: 0.7507 (p-90) REVERT: B 68 ARG cc_start: 0.8109 (ttt180) cc_final: 0.7888 (ttt180) REVERT: B 75 GLN cc_start: 0.7283 (mt0) cc_final: 0.6931 (mt0) REVERT: B 97 SER cc_start: 0.9234 (t) cc_final: 0.8826 (p) REVERT: B 134 ARG cc_start: 0.6982 (mmm-85) cc_final: 0.6701 (mtp-110) REVERT: B 176 GLN cc_start: 0.8763 (mt0) cc_final: 0.8447 (mt0) REVERT: B 228 ASP cc_start: 0.8307 (m-30) cc_final: 0.8064 (m-30) REVERT: B 237 ASN cc_start: 0.9048 (t0) cc_final: 0.8781 (t0) REVERT: B 247 ASP cc_start: 0.7841 (t0) cc_final: 0.7453 (t0) REVERT: B 304 ARG cc_start: 0.7733 (ttp-170) cc_final: 0.7491 (ttp80) REVERT: B 321 THR cc_start: 0.9297 (p) cc_final: 0.9062 (p) REVERT: A 16 SER cc_start: 0.8901 (p) cc_final: 0.8666 (p) REVERT: A 22 ASN cc_start: 0.8403 (m-40) cc_final: 0.8091 (m110) REVERT: A 214 CYS cc_start: 0.8533 (m) cc_final: 0.8031 (t) REVERT: A 312 LYS cc_start: 0.8308 (mttt) cc_final: 0.7964 (mmmt) REVERT: A 330 LYS cc_start: 0.8574 (mttt) cc_final: 0.8365 (mmtp) REVERT: G 27 ARG cc_start: 0.7354 (mtt-85) cc_final: 0.6339 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2074 time to fit residues: 85.6988 Evaluate side-chains 266 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.0030 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 GLN R 237 GLN R 310 ASN B 75 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN A 322 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.148895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.116818 restraints weight = 24357.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.123086 restraints weight = 11567.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.127207 restraints weight = 7169.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.130027 restraints weight = 5159.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.131764 restraints weight = 4079.678| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7134 Z= 0.138 Angle : 0.478 5.015 9673 Z= 0.258 Chirality : 0.037 0.141 1107 Planarity : 0.003 0.034 1224 Dihedral : 3.349 14.010 970 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.35 % Allowed : 14.82 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.28), residues: 881 helix: 1.50 (0.26), residues: 408 sheet: -2.81 (0.33), residues: 154 loop : -2.11 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.007 0.001 TYR G 40 PHE 0.013 0.001 PHE A 189 TRP 0.005 0.001 TRP R 117 HIS 0.002 0.001 HIS R 286 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7132) covalent geometry : angle 0.47737 ( 9669) SS BOND : bond 0.00150 ( 2) SS BOND : angle 1.28918 ( 4) hydrogen bonds : bond 0.03543 ( 378) hydrogen bonds : angle 3.99703 ( 1095) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 277 time to evaluate : 0.363 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8111 (mt-10) REVERT: R 237 GLN cc_start: 0.8326 (tp-100) cc_final: 0.7439 (tp40) REVERT: R 323 TRP cc_start: 0.8112 (p-90) cc_final: 0.7388 (p-90) REVERT: B 97 SER cc_start: 0.9227 (t) cc_final: 0.8839 (p) REVERT: B 134 ARG cc_start: 0.6967 (mmm-85) cc_final: 0.6681 (mtp-110) REVERT: B 176 GLN cc_start: 0.8739 (mt0) cc_final: 0.8419 (mt0) REVERT: B 228 ASP cc_start: 0.8250 (m-30) cc_final: 0.7993 (m-30) REVERT: B 247 ASP cc_start: 0.7878 (t0) cc_final: 0.7517 (t0) REVERT: B 304 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7535 (ttp80) REVERT: B 325 MET cc_start: 0.8017 (mmt) cc_final: 0.7130 (mmt) REVERT: A 16 SER cc_start: 0.8894 (p) cc_final: 0.8551 (p) REVERT: A 22 ASN cc_start: 0.8445 (m-40) cc_final: 0.8206 (m110) REVERT: A 25 GLU cc_start: 0.7587 (tp30) cc_final: 0.7375 (tp30) REVERT: A 330 LYS cc_start: 0.8476 (mttt) cc_final: 0.8191 (mmtp) REVERT: G 27 ARG cc_start: 0.7380 (mtt-85) cc_final: 0.7017 (mtt90) outliers start: 10 outliers final: 9 residues processed: 280 average time/residue: 0.1955 time to fit residues: 71.6254 Evaluate side-chains 278 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 269 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 27 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS B 230 ASN B 340 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.148044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.116507 restraints weight = 24619.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.122829 restraints weight = 11614.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.126978 restraints weight = 7133.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.129736 restraints weight = 5097.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131548 restraints weight = 4050.285| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7134 Z= 0.132 Angle : 0.476 7.155 9673 Z= 0.255 Chirality : 0.037 0.128 1107 Planarity : 0.004 0.046 1224 Dihedral : 3.460 24.593 970 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.16 % Allowed : 16.04 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.29), residues: 881 helix: 1.96 (0.26), residues: 407 sheet: -2.79 (0.34), residues: 156 loop : -1.97 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 155 TYR 0.012 0.001 TYR B 85 PHE 0.015 0.001 PHE A 189 TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7132) covalent geometry : angle 0.47592 ( 9669) SS BOND : bond 0.00208 ( 2) SS BOND : angle 0.68943 ( 4) hydrogen bonds : bond 0.03293 ( 378) hydrogen bonds : angle 3.93727 ( 1095) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 272 time to evaluate : 0.323 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: symmetry clash 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: symmetry clash REVERT: R 130 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8101 (mt-10) REVERT: R 323 TRP cc_start: 0.8168 (p-90) cc_final: 0.7362 (p-90) REVERT: B 57 LYS cc_start: 0.8250 (ptpt) cc_final: 0.8000 (ptmt) REVERT: B 97 SER cc_start: 0.9239 (t) cc_final: 0.8832 (p) REVERT: B 134 ARG cc_start: 0.6935 (mmm-85) cc_final: 0.6679 (mtp-110) REVERT: B 176 GLN cc_start: 0.8703 (mt0) cc_final: 0.8365 (mt0) REVERT: B 228 ASP cc_start: 0.8231 (m-30) cc_final: 0.7934 (m-30) REVERT: B 247 ASP cc_start: 0.7914 (t0) cc_final: 0.7501 (t0) REVERT: B 304 ARG cc_start: 0.7755 (ttp-170) cc_final: 0.7531 (ttp80) REVERT: B 325 MET cc_start: 0.7669 (mmt) cc_final: 0.7439 (mmt) REVERT: A 16 SER cc_start: 0.8885 (p) cc_final: 0.8649 (p) REVERT: A 22 ASN cc_start: 0.8496 (m-40) cc_final: 0.8232 (m110) REVERT: A 25 GLU cc_start: 0.7607 (tp30) cc_final: 0.7352 (tp30) REVERT: A 330 LYS cc_start: 0.8476 (mttt) cc_final: 0.8202 (mmtp) REVERT: A 333 GLN cc_start: 0.8774 (tt0) cc_final: 0.8001 (tp-100) REVERT: G 27 ARG cc_start: 0.7412 (mtt-85) cc_final: 0.7064 (mtt-85) REVERT: G 46 LYS cc_start: 0.8713 (mttp) cc_final: 0.8366 (mtpp) outliers start: 16 outliers final: 14 residues processed: 277 average time/residue: 0.1833 time to fit residues: 67.2071 Evaluate side-chains 279 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 265 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 4 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 GLN B 340 ASN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.145914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.114495 restraints weight = 24728.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.120672 restraints weight = 11605.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.124802 restraints weight = 7144.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.127529 restraints weight = 5124.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.129279 restraints weight = 4056.882| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7134 Z= 0.158 Angle : 0.482 7.269 9673 Z= 0.261 Chirality : 0.038 0.128 1107 Planarity : 0.003 0.038 1224 Dihedral : 3.492 14.176 970 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.02 % Allowed : 18.06 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.29), residues: 881 helix: 2.17 (0.26), residues: 407 sheet: -2.70 (0.34), residues: 161 loop : -1.94 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 232 TYR 0.008 0.001 TYR G 40 PHE 0.016 0.001 PHE A 189 TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7132) covalent geometry : angle 0.48202 ( 9669) SS BOND : bond 0.00134 ( 2) SS BOND : angle 1.15522 ( 4) hydrogen bonds : bond 0.03311 ( 378) hydrogen bonds : angle 3.95276 ( 1095) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 278 time to evaluate : 0.382 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8154 (mt-10) REVERT: R 150 GLN cc_start: 0.8269 (tp40) cc_final: 0.8030 (tp-100) REVERT: R 323 TRP cc_start: 0.8215 (p-90) cc_final: 0.7421 (p-90) REVERT: B 57 LYS cc_start: 0.8229 (ptpt) cc_final: 0.7966 (ptmt) REVERT: B 97 SER cc_start: 0.9289 (t) cc_final: 0.8922 (p) REVERT: B 134 ARG cc_start: 0.6979 (mmm-85) cc_final: 0.6722 (mtp-110) REVERT: B 228 ASP cc_start: 0.8259 (m-30) cc_final: 0.7935 (m-30) REVERT: B 247 ASP cc_start: 0.7962 (t0) cc_final: 0.7533 (t0) REVERT: B 304 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7529 (ttp80) REVERT: B 325 MET cc_start: 0.7941 (mmt) cc_final: 0.7388 (mmt) REVERT: A 16 SER cc_start: 0.8886 (p) cc_final: 0.8672 (p) REVERT: A 22 ASN cc_start: 0.8470 (m-40) cc_final: 0.8198 (m110) REVERT: A 25 GLU cc_start: 0.7622 (tp30) cc_final: 0.7371 (tp30) REVERT: A 283 LEU cc_start: 0.8252 (tp) cc_final: 0.7998 (tt) REVERT: A 286 CYS cc_start: 0.8244 (p) cc_final: 0.7616 (t) REVERT: A 289 GLU cc_start: 0.7366 (pm20) cc_final: 0.7060 (pm20) REVERT: A 330 LYS cc_start: 0.8464 (mttt) cc_final: 0.8196 (mmtp) REVERT: A 333 GLN cc_start: 0.8786 (tt0) cc_final: 0.8039 (tp-100) REVERT: G 27 ARG cc_start: 0.7420 (mtt-85) cc_final: 0.7048 (mtt-85) REVERT: G 46 LYS cc_start: 0.8698 (mttp) cc_final: 0.8364 (mtpp) outliers start: 15 outliers final: 15 residues processed: 283 average time/residue: 0.1870 time to fit residues: 69.4246 Evaluate side-chains 288 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 273 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.145430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.113924 restraints weight = 24891.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.120061 restraints weight = 11630.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.124138 restraints weight = 7169.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.126803 restraints weight = 5141.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128678 restraints weight = 4062.372| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7134 Z= 0.173 Angle : 0.498 6.986 9673 Z= 0.271 Chirality : 0.038 0.129 1107 Planarity : 0.004 0.039 1224 Dihedral : 3.672 28.827 970 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.96 % Allowed : 18.19 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.29), residues: 881 helix: 2.26 (0.25), residues: 407 sheet: -2.72 (0.35), residues: 162 loop : -1.84 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 232 TYR 0.008 0.001 TYR G 40 PHE 0.016 0.001 PHE A 189 TRP 0.005 0.001 TRP R 117 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7132) covalent geometry : angle 0.49730 ( 9669) SS BOND : bond 0.00471 ( 2) SS BOND : angle 1.58551 ( 4) hydrogen bonds : bond 0.03367 ( 378) hydrogen bonds : angle 3.97520 ( 1095) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 275 time to evaluate : 0.303 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: symmetry clash 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 130 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8123 (mt-10) REVERT: R 188 GLN cc_start: 0.7113 (tp40) cc_final: 0.6473 (tm-30) REVERT: R 323 TRP cc_start: 0.8270 (p-90) cc_final: 0.7425 (p-90) REVERT: B 57 LYS cc_start: 0.8250 (ptpt) cc_final: 0.7944 (ptmt) REVERT: B 97 SER cc_start: 0.9278 (t) cc_final: 0.8890 (p) REVERT: B 134 ARG cc_start: 0.6995 (mmm-85) cc_final: 0.6715 (mtp-110) REVERT: B 228 ASP cc_start: 0.8243 (m-30) cc_final: 0.7929 (m-30) REVERT: B 247 ASP cc_start: 0.7979 (t0) cc_final: 0.7526 (t0) REVERT: B 304 ARG cc_start: 0.7783 (ttp-170) cc_final: 0.7504 (ttp80) REVERT: B 325 MET cc_start: 0.7891 (mmt) cc_final: 0.7485 (mmt) REVERT: A 22 ASN cc_start: 0.8448 (m-40) cc_final: 0.8180 (m110) REVERT: A 25 GLU cc_start: 0.7616 (tp30) cc_final: 0.7377 (tp30) REVERT: A 248 LYS cc_start: 0.8842 (mttp) cc_final: 0.8451 (mtpt) REVERT: A 330 LYS cc_start: 0.8470 (mttt) cc_final: 0.8186 (mmtp) REVERT: G 27 ARG cc_start: 0.7471 (mtt-85) cc_final: 0.7206 (mtt-85) REVERT: G 46 LYS cc_start: 0.8697 (mttp) cc_final: 0.8367 (mtpp) outliers start: 22 outliers final: 21 residues processed: 280 average time/residue: 0.1997 time to fit residues: 73.5637 Evaluate side-chains 288 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 267 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 236 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.3980 chunk 48 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.146196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.115179 restraints weight = 24573.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.121367 restraints weight = 11396.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.125458 restraints weight = 6971.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.128071 restraints weight = 4978.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.129931 restraints weight = 3938.128| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7134 Z= 0.132 Angle : 0.490 8.918 9673 Z= 0.262 Chirality : 0.038 0.164 1107 Planarity : 0.003 0.041 1224 Dihedral : 3.558 17.303 970 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.70 % Allowed : 18.60 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.29), residues: 881 helix: 2.43 (0.25), residues: 407 sheet: -2.71 (0.37), residues: 146 loop : -1.82 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 232 TYR 0.008 0.001 TYR A 351 PHE 0.017 0.001 PHE A 189 TRP 0.005 0.001 TRP B 169 HIS 0.002 0.000 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7132) covalent geometry : angle 0.48885 ( 9669) SS BOND : bond 0.00299 ( 2) SS BOND : angle 1.55058 ( 4) hydrogen bonds : bond 0.03262 ( 378) hydrogen bonds : angle 3.89691 ( 1095) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 275 time to evaluate : 0.350 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8095 (mt-10) REVERT: R 150 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7955 (tp-100) REVERT: R 323 TRP cc_start: 0.8212 (p-90) cc_final: 0.7356 (p-90) REVERT: B 57 LYS cc_start: 0.8161 (ptpt) cc_final: 0.7825 (ptmt) REVERT: B 97 SER cc_start: 0.9360 (t) cc_final: 0.8922 (p) REVERT: B 134 ARG cc_start: 0.6979 (mmm-85) cc_final: 0.6690 (mtp-110) REVERT: B 163 ASP cc_start: 0.7411 (t0) cc_final: 0.7175 (t0) REVERT: B 228 ASP cc_start: 0.8211 (m-30) cc_final: 0.7874 (m-30) REVERT: B 247 ASP cc_start: 0.7887 (t0) cc_final: 0.7386 (t0) REVERT: B 304 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7499 (ttp80) REVERT: A 22 ASN cc_start: 0.8424 (m-40) cc_final: 0.8157 (m110) REVERT: A 25 GLU cc_start: 0.7610 (tp30) cc_final: 0.7371 (tp30) REVERT: A 214 CYS cc_start: 0.8509 (m) cc_final: 0.7690 (t) REVERT: A 248 LYS cc_start: 0.8850 (mttp) cc_final: 0.8438 (mtpt) REVERT: A 261 ASP cc_start: 0.8783 (p0) cc_final: 0.8542 (p0) REVERT: A 283 LEU cc_start: 0.8300 (tp) cc_final: 0.8056 (tt) REVERT: A 286 CYS cc_start: 0.8220 (p) cc_final: 0.7701 (t) REVERT: A 351 TYR cc_start: 0.7864 (m-10) cc_final: 0.7635 (m-10) REVERT: G 27 ARG cc_start: 0.7437 (mtt-85) cc_final: 0.7225 (mtt-85) REVERT: G 46 LYS cc_start: 0.8692 (mttp) cc_final: 0.8492 (mmmm) outliers start: 20 outliers final: 18 residues processed: 280 average time/residue: 0.1923 time to fit residues: 71.0995 Evaluate side-chains 287 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 269 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 236 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.145814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.114771 restraints weight = 24507.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.120966 restraints weight = 11441.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.124980 restraints weight = 7019.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.127548 restraints weight = 5036.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.129411 restraints weight = 3994.254| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7134 Z= 0.150 Angle : 0.486 6.292 9673 Z= 0.264 Chirality : 0.038 0.141 1107 Planarity : 0.003 0.045 1224 Dihedral : 3.703 33.651 970 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.70 % Allowed : 19.68 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.29), residues: 881 helix: 2.62 (0.25), residues: 401 sheet: -2.59 (0.37), residues: 153 loop : -1.70 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 232 TYR 0.008 0.001 TYR G 40 PHE 0.018 0.001 PHE A 189 TRP 0.005 0.001 TRP B 99 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7132) covalent geometry : angle 0.48535 ( 9669) SS BOND : bond 0.00065 ( 2) SS BOND : angle 1.61480 ( 4) hydrogen bonds : bond 0.03275 ( 378) hydrogen bonds : angle 3.91830 ( 1095) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 261 time to evaluate : 0.321 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8108 (mt-10) REVERT: R 150 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7959 (tp-100) REVERT: B 57 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7808 (ptmt) REVERT: B 97 SER cc_start: 0.9223 (t) cc_final: 0.8861 (p) REVERT: B 134 ARG cc_start: 0.6814 (mmm-85) cc_final: 0.6537 (mtp-110) REVERT: B 163 ASP cc_start: 0.7464 (t0) cc_final: 0.7225 (t0) REVERT: B 176 GLN cc_start: 0.8724 (mt0) cc_final: 0.8399 (mt0) REVERT: B 228 ASP cc_start: 0.8172 (m-30) cc_final: 0.7848 (m-30) REVERT: B 247 ASP cc_start: 0.7901 (t0) cc_final: 0.7390 (t0) REVERT: B 304 ARG cc_start: 0.7763 (ttp-170) cc_final: 0.7495 (ttp80) REVERT: B 325 MET cc_start: 0.7889 (mmt) cc_final: 0.7471 (mmt) REVERT: A 22 ASN cc_start: 0.8429 (m-40) cc_final: 0.8161 (m110) REVERT: A 214 CYS cc_start: 0.8507 (m) cc_final: 0.7689 (t) REVERT: A 248 LYS cc_start: 0.8870 (mttp) cc_final: 0.8469 (mtpt) REVERT: A 261 ASP cc_start: 0.8784 (p0) cc_final: 0.8520 (p0) REVERT: A 283 LEU cc_start: 0.8326 (tp) cc_final: 0.8105 (tt) REVERT: A 286 CYS cc_start: 0.8164 (p) cc_final: 0.7610 (t) outliers start: 20 outliers final: 18 residues processed: 265 average time/residue: 0.1898 time to fit residues: 66.7491 Evaluate side-chains 282 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 236 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.144679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.113712 restraints weight = 24540.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.119902 restraints weight = 11423.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.123935 restraints weight = 6966.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.126487 restraints weight = 4973.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.128373 restraints weight = 3952.441| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7134 Z= 0.169 Angle : 0.497 5.451 9673 Z= 0.272 Chirality : 0.038 0.128 1107 Planarity : 0.003 0.041 1224 Dihedral : 3.645 15.946 970 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.70 % Allowed : 19.68 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.29), residues: 881 helix: 2.57 (0.25), residues: 402 sheet: -2.58 (0.38), residues: 153 loop : -1.68 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 183 TYR 0.009 0.001 TYR G 40 PHE 0.018 0.001 PHE A 189 TRP 0.005 0.001 TRP B 99 HIS 0.005 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7132) covalent geometry : angle 0.49595 ( 9669) SS BOND : bond 0.00201 ( 2) SS BOND : angle 1.85051 ( 4) hydrogen bonds : bond 0.03345 ( 378) hydrogen bonds : angle 3.97286 ( 1095) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 259 time to evaluate : 0.338 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8130 (mt-10) REVERT: R 150 GLN cc_start: 0.8206 (tp-100) cc_final: 0.7954 (tp-100) REVERT: B 57 LYS cc_start: 0.8019 (ptpt) cc_final: 0.7706 (ptmt) REVERT: B 61 MET cc_start: 0.8984 (ppp) cc_final: 0.8520 (ppp) REVERT: B 97 SER cc_start: 0.9303 (t) cc_final: 0.8910 (p) REVERT: B 134 ARG cc_start: 0.6825 (mmm-85) cc_final: 0.6558 (mtp-110) REVERT: B 176 GLN cc_start: 0.8782 (mt0) cc_final: 0.8459 (mt0) REVERT: B 228 ASP cc_start: 0.8139 (m-30) cc_final: 0.7813 (m-30) REVERT: B 247 ASP cc_start: 0.7936 (t0) cc_final: 0.7461 (t0) REVERT: B 304 ARG cc_start: 0.7779 (ttp-170) cc_final: 0.7493 (ttp80) REVERT: A 22 ASN cc_start: 0.8447 (m-40) cc_final: 0.8178 (m110) REVERT: A 214 CYS cc_start: 0.8522 (m) cc_final: 0.7738 (t) REVERT: A 216 GLU cc_start: 0.8334 (tp30) cc_final: 0.7537 (tp30) REVERT: A 248 LYS cc_start: 0.8880 (mttp) cc_final: 0.8475 (mtpt) REVERT: A 289 GLU cc_start: 0.7302 (pm20) cc_final: 0.6957 (pm20) REVERT: A 298 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7394 (tt0) outliers start: 20 outliers final: 20 residues processed: 265 average time/residue: 0.1932 time to fit residues: 67.9217 Evaluate side-chains 275 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 236 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.144608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.113721 restraints weight = 24588.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.119958 restraints weight = 11443.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.123941 restraints weight = 6965.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.126614 restraints weight = 4993.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.128392 restraints weight = 3937.285| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7134 Z= 0.163 Angle : 0.501 5.127 9673 Z= 0.273 Chirality : 0.038 0.130 1107 Planarity : 0.004 0.049 1224 Dihedral : 3.827 34.719 970 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.96 % Allowed : 19.68 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.29), residues: 881 helix: 2.53 (0.25), residues: 402 sheet: -2.63 (0.37), residues: 158 loop : -1.65 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 232 TYR 0.009 0.001 TYR G 40 PHE 0.017 0.001 PHE A 189 TRP 0.005 0.001 TRP B 99 HIS 0.003 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7132) covalent geometry : angle 0.49925 ( 9669) SS BOND : bond 0.00093 ( 2) SS BOND : angle 2.06626 ( 4) hydrogen bonds : bond 0.03329 ( 378) hydrogen bonds : angle 3.98849 ( 1095) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 0.364 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8134 (mt-10) REVERT: R 150 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7967 (tp-100) REVERT: B 57 LYS cc_start: 0.8001 (ptpt) cc_final: 0.7703 (ptmt) REVERT: B 61 MET cc_start: 0.8969 (ppp) cc_final: 0.8530 (ppp) REVERT: B 97 SER cc_start: 0.9325 (t) cc_final: 0.8920 (p) REVERT: B 134 ARG cc_start: 0.6853 (mmm-85) cc_final: 0.6571 (mtp-110) REVERT: B 163 ASP cc_start: 0.7539 (t0) cc_final: 0.7276 (t0) REVERT: B 176 GLN cc_start: 0.8777 (mt0) cc_final: 0.8458 (mt0) REVERT: B 228 ASP cc_start: 0.8136 (m-30) cc_final: 0.7823 (m-30) REVERT: B 247 ASP cc_start: 0.7932 (t0) cc_final: 0.7488 (t0) REVERT: B 304 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7499 (ttp80) REVERT: A 22 ASN cc_start: 0.8451 (m-40) cc_final: 0.8212 (m110) REVERT: A 216 GLU cc_start: 0.8342 (tp30) cc_final: 0.7532 (tp30) REVERT: A 248 LYS cc_start: 0.8860 (mttp) cc_final: 0.8472 (mtpt) REVERT: A 283 LEU cc_start: 0.8264 (tp) cc_final: 0.8004 (tt) outliers start: 22 outliers final: 20 residues processed: 263 average time/residue: 0.1922 time to fit residues: 67.1618 Evaluate side-chains 272 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 236 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 0.0070 chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 16 optimal weight: 0.0970 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.146844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.115960 restraints weight = 24383.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.122269 restraints weight = 11284.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.126340 restraints weight = 6848.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.129048 restraints weight = 4853.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130880 restraints weight = 3814.637| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7134 Z= 0.113 Angle : 0.479 5.099 9673 Z= 0.259 Chirality : 0.037 0.131 1107 Planarity : 0.003 0.046 1224 Dihedral : 3.585 19.292 970 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.29 % Allowed : 20.08 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.30), residues: 881 helix: 2.74 (0.25), residues: 402 sheet: -2.59 (0.37), residues: 152 loop : -1.60 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 232 TYR 0.008 0.001 TYR B 59 PHE 0.016 0.001 PHE A 189 TRP 0.007 0.001 TRP B 169 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7132) covalent geometry : angle 0.47737 ( 9669) SS BOND : bond 0.00172 ( 2) SS BOND : angle 2.09979 ( 4) hydrogen bonds : bond 0.03122 ( 378) hydrogen bonds : angle 3.84116 ( 1095) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 250 time to evaluate : 0.358 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7979 (mt-10) REVERT: R 150 GLN cc_start: 0.8205 (tp-100) cc_final: 0.7951 (tp-100) REVERT: B 57 LYS cc_start: 0.7899 (ptpt) cc_final: 0.7602 (ptmt) REVERT: B 61 MET cc_start: 0.8933 (ppp) cc_final: 0.8501 (ppp) REVERT: B 97 SER cc_start: 0.9333 (t) cc_final: 0.8947 (p) REVERT: B 134 ARG cc_start: 0.6832 (mmm-85) cc_final: 0.6503 (mtp-110) REVERT: B 163 ASP cc_start: 0.7404 (t0) cc_final: 0.7130 (t0) REVERT: B 188 MET cc_start: 0.7606 (mmm) cc_final: 0.7365 (mmm) REVERT: B 228 ASP cc_start: 0.8116 (m-30) cc_final: 0.7831 (m-30) REVERT: B 247 ASP cc_start: 0.7875 (t0) cc_final: 0.7416 (t0) REVERT: B 304 ARG cc_start: 0.7744 (ttp-170) cc_final: 0.7481 (ttp80) REVERT: A 22 ASN cc_start: 0.8412 (m-40) cc_final: 0.8162 (m110) REVERT: A 214 CYS cc_start: 0.8437 (m) cc_final: 0.7771 (t) REVERT: A 216 GLU cc_start: 0.8373 (tp30) cc_final: 0.7661 (tp30) REVERT: A 248 LYS cc_start: 0.8851 (mttp) cc_final: 0.8430 (mtpt) REVERT: A 283 LEU cc_start: 0.8304 (tp) cc_final: 0.8048 (tt) outliers start: 17 outliers final: 17 residues processed: 256 average time/residue: 0.1914 time to fit residues: 64.7876 Evaluate side-chains 264 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 247 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 236 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 46 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 13 optimal weight: 0.0010 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 180 HIS A 304 GLN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.146982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.115808 restraints weight = 24550.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.122143 restraints weight = 11354.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.126067 restraints weight = 6894.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128903 restraints weight = 4941.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.130490 restraints weight = 3877.880| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7134 Z= 0.117 Angle : 0.484 4.964 9673 Z= 0.262 Chirality : 0.038 0.188 1107 Planarity : 0.004 0.047 1224 Dihedral : 3.688 36.673 970 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.29 % Allowed : 20.62 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.30), residues: 881 helix: 2.81 (0.25), residues: 403 sheet: -2.56 (0.37), residues: 152 loop : -1.53 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 183 TYR 0.011 0.001 TYR A 302 PHE 0.016 0.001 PHE A 189 TRP 0.006 0.001 TRP B 99 HIS 0.005 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 7132) covalent geometry : angle 0.48379 ( 9669) SS BOND : bond 0.00472 ( 2) SS BOND : angle 0.33412 ( 4) hydrogen bonds : bond 0.03068 ( 378) hydrogen bonds : angle 3.79725 ( 1095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2778.16 seconds wall clock time: 47 minutes 59.52 seconds (2879.52 seconds total)