Starting phenix.real_space_refine on Sat Jul 26 21:25:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqs_38587/07_2025/8xqs_38587.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqs_38587/07_2025/8xqs_38587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xqs_38587/07_2025/8xqs_38587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqs_38587/07_2025/8xqs_38587.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqs_38587/07_2025/8xqs_38587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqs_38587/07_2025/8xqs_38587.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 59 5.16 5 C 5681 2.51 5 N 1489 2.21 5 O 1635 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8867 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1813 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2194 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 3, 'TRANS': 267} Chain breaks: 2 Chain: "R" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'CLR': 1, 'FLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.62, per 1000 atoms: 0.63 Number of scatterers: 8867 At special positions: 0 Unit cell: (90.48, 118.56, 126.88, 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 59 16.00 F 3 9.00 O 1635 8.00 N 1489 7.00 C 5681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 41.1% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.779A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.665A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.744A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.662A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.140A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.551A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.799A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 37 Processing helix chain 'R' and resid 42 through 72 removed outlier: 3.757A pdb=" N PHE R 72 " --> pdb=" O VAL R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 77 Processing helix chain 'R' and resid 79 through 112 Processing helix chain 'R' and resid 116 through 124 removed outlier: 4.240A pdb=" N TRP R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 158 removed outlier: 3.951A pdb=" N VAL R 139 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY R 158 " --> pdb=" O ALA R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 215 removed outlier: 3.516A pdb=" N LEU R 181 " --> pdb=" O SER R 177 " (cutoff:3.500A) Proline residue: R 190 - end of helix Processing helix chain 'R' and resid 231 through 252 removed outlier: 4.099A pdb=" N ALA R 241 " --> pdb=" O PHE R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 284 removed outlier: 4.088A pdb=" N ILE R 262 " --> pdb=" O GLU R 258 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE R 263 " --> pdb=" O GLU R 259 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR R 272 " --> pdb=" O MET R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 4.586A pdb=" N SER R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.977A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.306A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.640A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.220A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.895A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.712A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.643A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.569A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.892A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.980A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.988A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 143 through 148 removed outlier: 3.645A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) 487 hydrogen bonds defined for protein. 1362 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2818 1.34 - 1.46: 2010 1.46 - 1.58: 4138 1.58 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 9053 Sorted by residual: bond pdb=" N FLF R 501 " pdb=" C1' FLF R 501 " ideal model delta sigma weight residual 1.377 1.415 -0.038 2.00e-02 2.50e+03 3.67e+00 bond pdb=" CB PRO R 73 " pdb=" CG PRO R 73 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.72e+00 bond pdb=" N FLF R 501 " pdb=" C6 FLF R 501 " ideal model delta sigma weight residual 1.378 1.409 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" CB VAL A 339 " pdb=" CG1 VAL A 339 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.94e+00 bond pdb=" C1 FLF R 501 " pdb=" C7 FLF R 501 " ideal model delta sigma weight residual 1.521 1.495 0.026 2.00e-02 2.50e+03 1.66e+00 ... (remaining 9048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 12007 1.77 - 3.54: 199 3.54 - 5.31: 34 5.31 - 7.07: 8 7.07 - 8.84: 4 Bond angle restraints: 12252 Sorted by residual: angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 108.34 115.02 -6.68 1.31e+00 5.83e-01 2.60e+01 angle pdb=" CA TYR A 230 " pdb=" CB TYR A 230 " pdb=" CG TYR A 230 " ideal model delta sigma weight residual 113.90 119.51 -5.61 1.80e+00 3.09e-01 9.72e+00 angle pdb=" N TYR S 223 " pdb=" CA TYR S 223 " pdb=" C TYR S 223 " ideal model delta sigma weight residual 109.81 115.96 -6.15 2.21e+00 2.05e-01 7.75e+00 angle pdb=" CA ASP B 258 " pdb=" CB ASP B 258 " pdb=" CG ASP B 258 " ideal model delta sigma weight residual 112.60 115.25 -2.65 1.00e+00 1.00e+00 7.00e+00 angle pdb=" CA LEU R 58 " pdb=" CB LEU R 58 " pdb=" CG LEU R 58 " ideal model delta sigma weight residual 116.30 125.14 -8.84 3.50e+00 8.16e-02 6.38e+00 ... (remaining 12247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 4543 14.74 - 29.48: 596 29.48 - 44.22: 203 44.22 - 58.97: 46 58.97 - 73.71: 3 Dihedral angle restraints: 5391 sinusoidal: 2143 harmonic: 3248 Sorted by residual: dihedral pdb=" CA LYS A 210 " pdb=" C LYS A 210 " pdb=" N TRP A 211 " pdb=" CA TRP A 211 " ideal model delta harmonic sigma weight residual 180.00 160.07 19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.31 18.69 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLU R 16 " pdb=" C GLU R 16 " pdb=" N PHE R 17 " pdb=" CA PHE R 17 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1214 0.061 - 0.121: 167 0.121 - 0.182: 16 0.182 - 0.243: 1 0.243 - 0.303: 1 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU C 50 " pdb=" CB LEU C 50 " pdb=" CD1 LEU C 50 " pdb=" CD2 LEU C 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA PRO R 73 " pdb=" N PRO R 73 " pdb=" C PRO R 73 " pdb=" CB PRO R 73 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 1396 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 59 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO C 60 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 72 " 0.052 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO R 73 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO R 73 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO R 73 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 258 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.04e+00 pdb=" C ASP B 258 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP B 258 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN B 259 " -0.013 2.00e-02 2.50e+03 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 151 2.64 - 3.21: 8322 3.21 - 3.77: 14449 3.77 - 4.34: 19586 4.34 - 4.90: 31664 Nonbonded interactions: 74172 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.078 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.123 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.174 3.040 nonbonded pdb=" OE2 GLU A 14 " pdb=" OG SER S 52 " model vdw 2.217 3.040 nonbonded pdb=" O ILE R 249 " pdb=" OG1 THR R 253 " model vdw 2.231 3.040 ... (remaining 74167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.340 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9055 Z= 0.170 Angle : 0.599 8.842 12256 Z= 0.317 Chirality : 0.043 0.303 1399 Planarity : 0.005 0.106 1524 Dihedral : 15.226 73.708 3283 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.31 % Allowed : 29.76 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1104 helix: 1.90 (0.25), residues: 422 sheet: -0.50 (0.31), residues: 278 loop : -1.05 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 297 HIS 0.008 0.001 HIS R 151 PHE 0.026 0.002 PHE R 186 TYR 0.014 0.002 TYR A 230 ARG 0.009 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.14340 ( 480) hydrogen bonds : angle 5.55966 ( 1362) SS BOND : bond 0.00273 ( 2) SS BOND : angle 0.68560 ( 4) covalent geometry : bond 0.00380 ( 9053) covalent geometry : angle 0.59894 (12252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 272 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 47 GLU cc_start: 0.7361 (mp0) cc_final: 0.7101 (mp0) REVERT: S 216 TYR cc_start: 0.8004 (m-80) cc_final: 0.7017 (m-80) REVERT: R 212 MET cc_start: 0.7471 (mmm) cc_final: 0.7209 (mmm) outliers start: 3 outliers final: 2 residues processed: 273 average time/residue: 0.2491 time to fit residues: 89.6628 Evaluate side-chains 281 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 279 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain S residue 162 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 239 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 ASN ** 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 = 0.3881 r_free = 0.3881 target = 0.144004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124838 restraints weight = 13949.261| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.50 r_work: 0.3496 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9055 Z= 0.212 Angle : 0.578 8.988 12256 Z= 0.310 Chirality : 0.043 0.202 1399 Planarity : 0.004 0.071 1524 Dihedral : 5.759 51.949 1273 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.63 % Allowed : 25.13 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1104 helix: 1.87 (0.25), residues: 427 sheet: -0.62 (0.30), residues: 289 loop : -1.02 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 169 HIS 0.005 0.001 HIS A 322 PHE 0.017 0.002 PHE R 17 TYR 0.019 0.002 TYR S 178 ARG 0.006 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04668 ( 480) hydrogen bonds : angle 4.73272 ( 1362) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.71123 ( 4) covalent geometry : bond 0.00454 ( 9053) covalent geometry : angle 0.57840 (12252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8625 (m-10) cc_final: 0.8312 (m-10) REVERT: A 350 ASP cc_start: 0.7900 (t0) cc_final: 0.7630 (t0) REVERT: B 83 ASP cc_start: 0.8092 (t0) cc_final: 0.7550 (t0) REVERT: B 258 ASP cc_start: 0.7734 (t0) cc_final: 0.7442 (t0) REVERT: B 290 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7215 (t0) REVERT: C 42 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7319 (tm-30) REVERT: C 47 GLU cc_start: 0.7180 (mp0) cc_final: 0.6852 (mp0) REVERT: S 191 PHE cc_start: 0.7304 (m-10) cc_final: 0.7078 (m-10) REVERT: R 16 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6970 (tm-30) REVERT: R 186 PHE cc_start: 0.7153 (t80) cc_final: 0.6940 (t80) REVERT: R 212 MET cc_start: 0.7617 (mmm) cc_final: 0.7377 (mpp) outliers start: 45 outliers final: 31 residues processed: 284 average time/residue: 0.2194 time to fit residues: 84.3628 Evaluate side-chains 298 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 266 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 60 TRP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 187 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.144331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125346 restraints weight = 14160.076| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.43 r_work: 0.3513 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9055 Z= 0.171 Angle : 0.543 8.463 12256 Z= 0.289 Chirality : 0.042 0.186 1399 Planarity : 0.004 0.059 1524 Dihedral : 5.419 52.833 1273 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.43 % Allowed : 24.61 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1104 helix: 1.96 (0.25), residues: 421 sheet: -0.55 (0.30), residues: 283 loop : -1.05 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 211 HIS 0.005 0.001 HIS A 322 PHE 0.015 0.002 PHE R 17 TYR 0.017 0.002 TYR S 178 ARG 0.004 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 480) hydrogen bonds : angle 4.55840 ( 1362) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.71849 ( 4) covalent geometry : bond 0.00367 ( 9053) covalent geometry : angle 0.54265 (12252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 211 TRP cc_start: 0.8058 (p-90) cc_final: 0.7696 (p-90) REVERT: A 215 PHE cc_start: 0.8675 (m-80) cc_final: 0.7881 (m-80) REVERT: A 267 PHE cc_start: 0.8615 (m-10) cc_final: 0.8152 (m-10) REVERT: A 350 ASP cc_start: 0.7880 (t0) cc_final: 0.7535 (t0) REVERT: B 49 ARG cc_start: 0.7890 (mpt180) cc_final: 0.7092 (mpt180) REVERT: B 83 ASP cc_start: 0.8121 (t0) cc_final: 0.7626 (t0) REVERT: B 134 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8113 (mtm-85) REVERT: B 269 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7530 (mm) REVERT: C 42 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7244 (tm-30) REVERT: C 47 GLU cc_start: 0.7164 (mp0) cc_final: 0.6833 (mp0) REVERT: S 59 TYR cc_start: 0.7202 (m-10) cc_final: 0.6874 (m-10) REVERT: S 87 ARG cc_start: 0.7413 (ptt180) cc_final: 0.7052 (ptt180) REVERT: S 135 VAL cc_start: 0.8458 (p) cc_final: 0.8218 (t) REVERT: S 191 PHE cc_start: 0.7428 (m-10) cc_final: 0.7181 (m-10) REVERT: R 123 LYS cc_start: 0.6597 (OUTLIER) cc_final: 0.6020 (mmmt) REVERT: R 212 MET cc_start: 0.7670 (mmm) cc_final: 0.7394 (mpp) outliers start: 43 outliers final: 31 residues processed: 280 average time/residue: 0.2140 time to fit residues: 80.9809 Evaluate side-chains 288 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 255 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 60 TRP Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 123 LYS Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 182 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.144358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.125812 restraints weight = 13969.487| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.36 r_work: 0.3518 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9055 Z= 0.166 Angle : 0.549 9.376 12256 Z= 0.288 Chirality : 0.041 0.183 1399 Planarity : 0.004 0.050 1524 Dihedral : 5.430 54.252 1273 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.05 % Allowed : 23.79 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1104 helix: 1.97 (0.24), residues: 420 sheet: -0.55 (0.30), residues: 287 loop : -1.04 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.005 0.001 HIS A 322 PHE 0.015 0.002 PHE R 186 TYR 0.017 0.002 TYR S 178 ARG 0.004 0.000 ARG R 55 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 480) hydrogen bonds : angle 4.50821 ( 1362) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.70639 ( 4) covalent geometry : bond 0.00355 ( 9053) covalent geometry : angle 0.54850 (12252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 260 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.8241 (m) cc_final: 0.7936 (p) REVERT: A 215 PHE cc_start: 0.8595 (m-80) cc_final: 0.7917 (m-80) REVERT: A 216 GLU cc_start: 0.7330 (tt0) cc_final: 0.7112 (tm-30) REVERT: A 267 PHE cc_start: 0.8638 (m-10) cc_final: 0.8217 (m-10) REVERT: A 350 ASP cc_start: 0.7866 (t0) cc_final: 0.7485 (t0) REVERT: B 46 ARG cc_start: 0.7604 (mtm110) cc_final: 0.7366 (mtm-85) REVERT: B 49 ARG cc_start: 0.7824 (mpt180) cc_final: 0.6983 (mpt180) REVERT: B 83 ASP cc_start: 0.8079 (t0) cc_final: 0.7604 (t0) REVERT: B 134 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.8122 (mtm-85) REVERT: B 269 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7548 (mm) REVERT: C 21 MET cc_start: 0.6627 (mpp) cc_final: 0.6422 (mpp) REVERT: C 47 GLU cc_start: 0.7146 (mp0) cc_final: 0.6850 (mp0) REVERT: S 59 TYR cc_start: 0.7183 (m-10) cc_final: 0.6865 (m-10) REVERT: S 117 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6691 (tt) REVERT: S 135 VAL cc_start: 0.8513 (p) cc_final: 0.8231 (t) REVERT: S 174 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: S 191 PHE cc_start: 0.7427 (m-10) cc_final: 0.7170 (m-10) REVERT: S 192 SER cc_start: 0.7801 (OUTLIER) cc_final: 0.7542 (p) REVERT: R 123 LYS cc_start: 0.6573 (OUTLIER) cc_final: 0.6019 (mmmt) REVERT: R 212 MET cc_start: 0.7635 (mmm) cc_final: 0.7399 (mmp) outliers start: 49 outliers final: 38 residues processed: 284 average time/residue: 0.2168 time to fit residues: 83.2821 Evaluate side-chains 301 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 56 ILE Chi-restraints excluded: chain R residue 60 TRP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 123 LYS Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 253 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.144315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125592 restraints weight = 13963.604| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.41 r_work: 0.3484 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9055 Z= 0.163 Angle : 0.542 8.443 12256 Z= 0.287 Chirality : 0.041 0.181 1399 Planarity : 0.004 0.048 1524 Dihedral : 5.368 54.225 1273 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.46 % Allowed : 24.10 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1104 helix: 1.99 (0.24), residues: 420 sheet: -0.61 (0.30), residues: 294 loop : -0.98 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 98 HIS 0.005 0.001 HIS A 322 PHE 0.017 0.002 PHE R 17 TYR 0.016 0.002 TYR S 178 ARG 0.005 0.000 ARG R 55 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 480) hydrogen bonds : angle 4.47311 ( 1362) SS BOND : bond 0.00309 ( 2) SS BOND : angle 0.72372 ( 4) covalent geometry : bond 0.00351 ( 9053) covalent geometry : angle 0.54148 (12252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 260 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.8243 (m) cc_final: 0.7943 (p) REVERT: A 215 PHE cc_start: 0.8618 (m-80) cc_final: 0.7982 (m-80) REVERT: A 267 PHE cc_start: 0.8643 (m-10) cc_final: 0.8308 (m-10) REVERT: A 350 ASP cc_start: 0.7886 (t0) cc_final: 0.7526 (t0) REVERT: B 46 ARG cc_start: 0.7666 (mtm110) cc_final: 0.7326 (mtm-85) REVERT: B 49 ARG cc_start: 0.7795 (mpt180) cc_final: 0.7023 (mpt180) REVERT: B 83 ASP cc_start: 0.8029 (t0) cc_final: 0.7609 (t0) REVERT: B 134 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.8110 (mtm-85) REVERT: C 47 GLU cc_start: 0.7209 (mp0) cc_final: 0.6924 (mp0) REVERT: S 59 TYR cc_start: 0.7193 (m-10) cc_final: 0.6913 (m-10) REVERT: S 135 VAL cc_start: 0.8382 (p) cc_final: 0.8104 (t) REVERT: S 162 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7763 (tt) REVERT: S 191 PHE cc_start: 0.7399 (m-10) cc_final: 0.7125 (m-10) REVERT: S 192 SER cc_start: 0.7824 (OUTLIER) cc_final: 0.7573 (p) REVERT: R 123 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6061 (mmmt) outliers start: 53 outliers final: 40 residues processed: 288 average time/residue: 0.2135 time to fit residues: 83.8343 Evaluate side-chains 298 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 255 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 56 ILE Chi-restraints excluded: chain R residue 60 TRP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 123 LYS Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 253 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 27 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.0170 chunk 18 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 266 HIS C 24 ASN ** R 260 ASN ** 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 = 0.3892 r_free = 0.3892 target = 0.144999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.126348 restraints weight = 13900.597| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.40 r_work: 0.3495 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9055 Z= 0.146 Angle : 0.538 7.969 12256 Z= 0.282 Chirality : 0.041 0.177 1399 Planarity : 0.004 0.047 1524 Dihedral : 5.342 55.138 1273 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.36 % Allowed : 24.41 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1104 helix: 1.99 (0.24), residues: 423 sheet: -0.51 (0.31), residues: 289 loop : -0.86 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.005 0.001 HIS R 151 PHE 0.020 0.002 PHE R 17 TYR 0.015 0.001 TYR S 178 ARG 0.005 0.000 ARG R 55 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 480) hydrogen bonds : angle 4.41022 ( 1362) SS BOND : bond 0.00282 ( 2) SS BOND : angle 0.59034 ( 4) covalent geometry : bond 0.00314 ( 9053) covalent geometry : angle 0.53786 (12252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 260 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.8319 (m) cc_final: 0.8000 (p) REVERT: A 215 PHE cc_start: 0.8619 (m-80) cc_final: 0.8050 (m-80) REVERT: A 267 PHE cc_start: 0.8656 (m-10) cc_final: 0.8302 (m-10) REVERT: A 350 ASP cc_start: 0.7862 (t0) cc_final: 0.7521 (t0) REVERT: B 46 ARG cc_start: 0.7662 (mtm110) cc_final: 0.7313 (mtm-85) REVERT: B 49 ARG cc_start: 0.7778 (mpt180) cc_final: 0.7011 (mpt180) REVERT: B 70 LEU cc_start: 0.8533 (tp) cc_final: 0.8257 (tt) REVERT: B 83 ASP cc_start: 0.7985 (t0) cc_final: 0.7667 (t70) REVERT: B 134 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8073 (mtm-85) REVERT: B 308 LEU cc_start: 0.8211 (mp) cc_final: 0.7986 (tp) REVERT: C 47 GLU cc_start: 0.7194 (mp0) cc_final: 0.6909 (mp0) REVERT: S 59 TYR cc_start: 0.7126 (m-10) cc_final: 0.6872 (m-10) REVERT: S 191 PHE cc_start: 0.7392 (m-10) cc_final: 0.7115 (m-10) REVERT: S 192 SER cc_start: 0.7841 (OUTLIER) cc_final: 0.7587 (p) REVERT: R 123 LYS cc_start: 0.6706 (OUTLIER) cc_final: 0.6086 (mmmt) REVERT: R 270 MET cc_start: 0.5227 (ptm) cc_final: 0.4904 (ttp) outliers start: 52 outliers final: 42 residues processed: 290 average time/residue: 0.2188 time to fit residues: 86.1423 Evaluate side-chains 293 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 60 TRP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 123 LYS Chi-restraints excluded: chain R residue 124 TRP Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 253 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 5 optimal weight: 0.0270 chunk 6 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN B 266 HIS ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 ASN ** 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 = 0.3893 r_free = 0.3893 target = 0.145109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.126475 restraints weight = 14149.564| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.40 r_work: 0.3494 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9055 Z= 0.153 Angle : 0.552 8.377 12256 Z= 0.287 Chirality : 0.041 0.186 1399 Planarity : 0.004 0.047 1524 Dihedral : 5.187 55.366 1271 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.15 % Allowed : 25.13 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1104 helix: 2.14 (0.24), residues: 416 sheet: -0.44 (0.31), residues: 282 loop : -0.84 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.005 0.001 HIS R 151 PHE 0.021 0.002 PHE R 17 TYR 0.015 0.001 TYR S 178 ARG 0.004 0.000 ARG R 55 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 480) hydrogen bonds : angle 4.40213 ( 1362) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.70545 ( 4) covalent geometry : bond 0.00332 ( 9053) covalent geometry : angle 0.55237 (12252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 263 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.8313 (m) cc_final: 0.7989 (p) REVERT: A 215 PHE cc_start: 0.8605 (m-80) cc_final: 0.8017 (m-80) REVERT: A 267 PHE cc_start: 0.8646 (m-10) cc_final: 0.8275 (m-10) REVERT: A 298 GLU cc_start: 0.6427 (tp30) cc_final: 0.5736 (tp30) REVERT: A 339 VAL cc_start: 0.7817 (t) cc_final: 0.7593 (t) REVERT: A 350 ASP cc_start: 0.7848 (t0) cc_final: 0.7518 (t0) REVERT: B 46 ARG cc_start: 0.7644 (mtm110) cc_final: 0.7312 (mtm-85) REVERT: B 49 ARG cc_start: 0.7805 (mpt180) cc_final: 0.7052 (mpt180) REVERT: B 70 LEU cc_start: 0.8526 (tp) cc_final: 0.8228 (tt) REVERT: B 83 ASP cc_start: 0.8017 (t0) cc_final: 0.7619 (t0) REVERT: B 134 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.8090 (mtm-85) REVERT: B 188 MET cc_start: 0.7474 (tpp) cc_final: 0.6840 (tpp) REVERT: B 308 LEU cc_start: 0.8211 (mp) cc_final: 0.7991 (tp) REVERT: C 47 GLU cc_start: 0.7142 (mp0) cc_final: 0.6906 (mp0) REVERT: S 59 TYR cc_start: 0.7105 (m-10) cc_final: 0.6877 (m-10) REVERT: S 191 PHE cc_start: 0.7426 (m-10) cc_final: 0.7164 (m-10) REVERT: S 192 SER cc_start: 0.7825 (OUTLIER) cc_final: 0.7580 (p) REVERT: R 16 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6905 (tm-30) REVERT: R 72 PHE cc_start: 0.6417 (t80) cc_final: 0.6208 (t80) REVERT: R 123 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.6111 (mmmt) outliers start: 50 outliers final: 38 residues processed: 291 average time/residue: 0.2134 time to fit residues: 84.4902 Evaluate side-chains 301 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 60 TRP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 123 LYS Chi-restraints excluded: chain R residue 124 TRP Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 253 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 241 ASN B 266 HIS ** S 39 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 = 0.3887 r_free = 0.3887 target = 0.144592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.126001 restraints weight = 14254.130| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.39 r_work: 0.3493 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9055 Z= 0.169 Angle : 0.572 10.765 12256 Z= 0.298 Chirality : 0.042 0.251 1399 Planarity : 0.004 0.048 1524 Dihedral : 5.239 55.809 1271 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.33 % Allowed : 25.13 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1104 helix: 2.12 (0.24), residues: 416 sheet: -0.48 (0.31), residues: 282 loop : -0.88 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.005 0.001 HIS A 322 PHE 0.022 0.002 PHE R 17 TYR 0.016 0.002 TYR S 178 ARG 0.004 0.000 ARG R 55 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 480) hydrogen bonds : angle 4.47632 ( 1362) SS BOND : bond 0.00334 ( 2) SS BOND : angle 0.79300 ( 4) covalent geometry : bond 0.00370 ( 9053) covalent geometry : angle 0.57188 (12252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 269 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.8305 (m) cc_final: 0.7983 (p) REVERT: A 215 PHE cc_start: 0.8589 (m-80) cc_final: 0.8040 (m-80) REVERT: A 267 PHE cc_start: 0.8657 (m-10) cc_final: 0.8280 (m-10) REVERT: A 298 GLU cc_start: 0.6410 (tp30) cc_final: 0.5716 (tp30) REVERT: A 339 VAL cc_start: 0.7833 (t) cc_final: 0.7618 (t) REVERT: A 350 ASP cc_start: 0.7869 (t0) cc_final: 0.7514 (t0) REVERT: B 46 ARG cc_start: 0.7633 (mtm110) cc_final: 0.7296 (mtm-85) REVERT: B 49 ARG cc_start: 0.7805 (mpt180) cc_final: 0.7066 (mpt180) REVERT: B 70 LEU cc_start: 0.8538 (tp) cc_final: 0.8214 (tt) REVERT: B 83 ASP cc_start: 0.8023 (t0) cc_final: 0.7798 (t0) REVERT: B 134 ARG cc_start: 0.8349 (mtm-85) cc_final: 0.8059 (mtm-85) REVERT: C 21 MET cc_start: 0.6748 (mpp) cc_final: 0.6511 (mpp) REVERT: C 47 GLU cc_start: 0.7135 (mp0) cc_final: 0.6763 (mp0) REVERT: S 59 TYR cc_start: 0.7117 (m-10) cc_final: 0.6888 (m-10) REVERT: S 191 PHE cc_start: 0.7462 (m-10) cc_final: 0.7242 (m-10) REVERT: S 192 SER cc_start: 0.7829 (OUTLIER) cc_final: 0.7592 (p) REVERT: R 16 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6114 (tm-30) REVERT: R 58 LEU cc_start: 0.7716 (tp) cc_final: 0.7468 (tt) REVERT: R 123 LYS cc_start: 0.6664 (OUTLIER) cc_final: 0.6121 (mmmt) REVERT: R 270 MET cc_start: 0.5198 (ptm) cc_final: 0.4838 (ttp) outliers start: 42 outliers final: 38 residues processed: 296 average time/residue: 0.2134 time to fit residues: 87.2254 Evaluate side-chains 298 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 258 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 60 TRP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 123 LYS Chi-restraints excluded: chain R residue 124 TRP Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 253 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 72 optimal weight: 0.0570 chunk 34 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN B 266 HIS ** S 39 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 = 0.3894 r_free = 0.3894 target = 0.145231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.126506 restraints weight = 14108.056| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.43 r_work: 0.3498 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9055 Z= 0.150 Angle : 0.568 7.860 12256 Z= 0.295 Chirality : 0.042 0.226 1399 Planarity : 0.004 0.047 1524 Dihedral : 5.264 56.433 1271 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.22 % Allowed : 25.85 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1104 helix: 2.18 (0.24), residues: 415 sheet: -0.46 (0.31), residues: 282 loop : -0.87 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 89 HIS 0.005 0.001 HIS A 322 PHE 0.022 0.002 PHE R 17 TYR 0.016 0.001 TYR S 223 ARG 0.003 0.000 ARG R 55 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 480) hydrogen bonds : angle 4.45908 ( 1362) SS BOND : bond 0.00374 ( 2) SS BOND : angle 0.90315 ( 4) covalent geometry : bond 0.00331 ( 9053) covalent geometry : angle 0.56810 (12252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 263 time to evaluate : 1.045 Fit side-chains REVERT: A 190 THR cc_start: 0.8307 (m) cc_final: 0.7985 (p) REVERT: A 215 PHE cc_start: 0.8606 (m-80) cc_final: 0.7996 (m-80) REVERT: A 267 PHE cc_start: 0.8646 (m-10) cc_final: 0.8256 (m-10) REVERT: A 298 GLU cc_start: 0.6469 (tp30) cc_final: 0.6190 (tp30) REVERT: A 339 VAL cc_start: 0.7818 (t) cc_final: 0.7593 (t) REVERT: A 350 ASP cc_start: 0.7875 (t0) cc_final: 0.7519 (t0) REVERT: B 46 ARG cc_start: 0.7674 (mtm110) cc_final: 0.7287 (mtm-85) REVERT: B 49 ARG cc_start: 0.7800 (mpt180) cc_final: 0.7043 (mpt180) REVERT: B 83 ASP cc_start: 0.7993 (t0) cc_final: 0.7748 (t0) REVERT: B 118 ASP cc_start: 0.7910 (p0) cc_final: 0.7629 (p0) REVERT: B 134 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.8044 (mtm-85) REVERT: C 21 MET cc_start: 0.6778 (mpp) cc_final: 0.6490 (mpp) REVERT: C 47 GLU cc_start: 0.7084 (mp0) cc_final: 0.6746 (mp0) REVERT: S 59 TYR cc_start: 0.7117 (m-10) cc_final: 0.6856 (m-10) REVERT: S 84 THR cc_start: 0.8183 (p) cc_final: 0.7832 (t) REVERT: S 174 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7638 (pt0) REVERT: R 16 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6151 (tm-30) REVERT: R 123 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.6141 (mmmt) REVERT: R 270 MET cc_start: 0.5248 (ptm) cc_final: 0.4916 (ttp) outliers start: 41 outliers final: 39 residues processed: 289 average time/residue: 0.2162 time to fit residues: 85.6068 Evaluate side-chains 295 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 254 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 60 TRP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 123 LYS Chi-restraints excluded: chain R residue 124 TRP Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 253 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 chunk 79 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS S 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.145429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126830 restraints weight = 13954.811| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.37 r_work: 0.3506 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9055 Z= 0.154 Angle : 0.577 7.985 12256 Z= 0.299 Chirality : 0.042 0.210 1399 Planarity : 0.004 0.047 1524 Dihedral : 5.282 56.391 1271 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.33 % Allowed : 26.16 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1104 helix: 2.16 (0.24), residues: 415 sheet: -0.47 (0.30), residues: 286 loop : -0.90 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 89 HIS 0.005 0.001 HIS A 322 PHE 0.019 0.002 PHE R 186 TYR 0.015 0.001 TYR S 178 ARG 0.004 0.000 ARG R 55 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 480) hydrogen bonds : angle 4.47739 ( 1362) SS BOND : bond 0.00307 ( 2) SS BOND : angle 0.84344 ( 4) covalent geometry : bond 0.00343 ( 9053) covalent geometry : angle 0.57689 (12252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.8292 (m) cc_final: 0.7965 (p) REVERT: A 210 LYS cc_start: 0.7064 (ptpp) cc_final: 0.6765 (ptmm) REVERT: A 267 PHE cc_start: 0.8603 (m-10) cc_final: 0.8231 (m-10) REVERT: A 350 ASP cc_start: 0.7815 (t0) cc_final: 0.7477 (t0) REVERT: B 49 ARG cc_start: 0.7852 (mpt180) cc_final: 0.7127 (mpt180) REVERT: B 134 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.8040 (mtm-85) REVERT: C 21 MET cc_start: 0.6753 (mpp) cc_final: 0.6446 (mpp) REVERT: C 47 GLU cc_start: 0.7040 (mp0) cc_final: 0.6695 (mp0) REVERT: S 59 TYR cc_start: 0.7058 (m-10) cc_final: 0.6850 (m-10) REVERT: S 84 THR cc_start: 0.8230 (p) cc_final: 0.7848 (t) REVERT: R 16 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6056 (tm-30) REVERT: R 123 LYS cc_start: 0.6736 (OUTLIER) cc_final: 0.6189 (mmmt) REVERT: R 270 MET cc_start: 0.5147 (ptm) cc_final: 0.4775 (ttp) outliers start: 42 outliers final: 41 residues processed: 286 average time/residue: 0.2190 time to fit residues: 85.6150 Evaluate side-chains 300 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 60 TRP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 123 LYS Chi-restraints excluded: chain R residue 124 TRP Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 253 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 60 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.144884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126079 restraints weight = 14131.371| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.43 r_work: 0.3491 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9055 Z= 0.167 Angle : 0.600 8.633 12256 Z= 0.309 Chirality : 0.042 0.202 1399 Planarity : 0.004 0.048 1524 Dihedral : 5.335 56.742 1271 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.63 % Allowed : 26.06 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1104 helix: 2.15 (0.24), residues: 415 sheet: -0.50 (0.30), residues: 286 loop : -0.90 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.005 0.001 HIS A 322 PHE 0.019 0.002 PHE R 186 TYR 0.016 0.002 TYR S 178 ARG 0.003 0.000 ARG R 55 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 480) hydrogen bonds : angle 4.50758 ( 1362) SS BOND : bond 0.00378 ( 2) SS BOND : angle 1.00470 ( 4) covalent geometry : bond 0.00372 ( 9053) covalent geometry : angle 0.59939 (12252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4412.31 seconds wall clock time: 76 minutes 56.81 seconds (4616.81 seconds total)