Starting phenix.real_space_refine on Sat Aug 23 01:58:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6osa_20181/08_2025/6osa_20181.cif Found real_map, /net/cci-nas-00/data/ceres_data/6osa_20181/08_2025/6osa_20181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6osa_20181/08_2025/6osa_20181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6osa_20181/08_2025/6osa_20181.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6osa_20181/08_2025/6osa_20181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6osa_20181/08_2025/6osa_20181.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2130 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 4672 2.51 5 N 1256 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7338 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2532 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 10, 'TRANS': 310} Chain breaks: 1 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2585 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 410 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.59, per 1000 atoms: 0.22 Number of scatterers: 7338 At special positions: 0 Unit cell: (78.44, 114.48, 112.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1356 8.00 N 1256 7.00 C 4672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 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: 0.50 Conformation dependent library (CDL) restraints added in 274.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1772 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 48.3% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 97 through 129 removed outlier: 3.987A pdb=" N VAL R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 139 through 171 Processing helix chain 'R' and resid 172 through 180 removed outlier: 3.514A pdb=" N ALA R 176 " --> pdb=" O HIS R 172 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 200 removed outlier: 3.886A pdb=" N ALA R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 206 Processing helix chain 'R' and resid 229 through 273 Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 280 through 329 removed outlier: 4.211A pdb=" N GLN R 296 " --> pdb=" O PRO R 292 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.803A pdb=" N ILE R 329 " --> pdb=" O MET R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 356 removed outlier: 4.025A pdb=" N SER R 356 " --> pdb=" O LEU R 352 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 368 removed outlier: 4.141A pdb=" N ILE R 362 " --> pdb=" O THR R 358 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU R 363 " --> pdb=" O ILE R 359 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR R 364 " --> pdb=" O ASN R 360 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 383 removed outlier: 3.593A pdb=" N HIS R 373 " --> pdb=" O ALA R 369 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE R 374 " --> pdb=" O ASN R 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.961A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.169A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.563A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.914A 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 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.105A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.733A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.520A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.800A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.644A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'R' and resid 207 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.765A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52 removed outlier: 4.072A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.732A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.348A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.615A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.857A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.261A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.759A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1227 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: 1.04 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2372 1.35 - 1.48: 1912 1.48 - 1.61: 3125 1.61 - 1.74: 0 1.74 - 1.86: 77 Bond restraints: 7486 Sorted by residual: bond pdb=" C LEU R 317 " pdb=" N PRO R 318 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.28e-02 6.10e+03 1.71e+01 bond pdb=" C MET R 120 " pdb=" N PRO R 121 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.20e-02 6.94e+03 1.44e+01 bond pdb=" SD MET B 61 " pdb=" CE MET B 61 " ideal model delta sigma weight residual 1.791 1.736 0.055 2.50e-02 1.60e+03 4.78e+00 bond pdb=" CG LEU B 51 " pdb=" CD2 LEU B 51 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.37e+00 bond pdb=" CG LEU B 146 " pdb=" CD1 LEU B 146 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.36e+00 ... (remaining 7481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 10002 3.52 - 7.05: 128 7.05 - 10.57: 10 10.57 - 14.10: 3 14.10 - 17.62: 1 Bond angle restraints: 10144 Sorted by residual: angle pdb=" CA LEU R 263 " pdb=" CB LEU R 263 " pdb=" CG LEU R 263 " ideal model delta sigma weight residual 116.30 133.92 -17.62 3.50e+00 8.16e-02 2.54e+01 angle pdb=" C HIS B 142 " pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta sigma weight residual 122.08 128.54 -6.46 1.47e+00 4.63e-01 1.93e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.57e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 122.07 127.69 -5.62 1.43e+00 4.89e-01 1.55e+01 angle pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " pdb=" CG LEU B 336 " ideal model delta sigma weight residual 116.30 130.04 -13.74 3.50e+00 8.16e-02 1.54e+01 ... (remaining 10139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 4167 16.15 - 32.30: 234 32.30 - 48.45: 40 48.45 - 64.60: 3 64.60 - 80.75: 8 Dihedral angle restraints: 4452 sinusoidal: 1719 harmonic: 2733 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 173.75 -80.75 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE L 12 " pdb=" C ILE L 12 " pdb=" N LEU L 13 " pdb=" CA LEU L 13 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 4449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 826 0.053 - 0.106: 259 0.106 - 0.160: 68 0.160 - 0.213: 14 0.213 - 0.266: 4 Chirality restraints: 1171 Sorted by residual: chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 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 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1168 not shown) Planarity restraints: 1277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 243 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.39e+00 pdb=" C MET R 243 " -0.053 2.00e-02 2.50e+03 pdb=" O MET R 243 " 0.020 2.00e-02 2.50e+03 pdb=" N SER R 244 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 124 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C LEU R 124 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU R 124 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR R 125 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO C 49 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.036 5.00e-02 4.00e+02 ... (remaining 1274 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1009 2.75 - 3.29: 6844 3.29 - 3.82: 12240 3.82 - 4.36: 13986 4.36 - 4.90: 24939 Nonbonded interactions: 59018 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.309 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.319 3.040 nonbonded pdb=" O GLY B 182 " pdb=" NZ LYS B 209 " model vdw 2.329 3.120 nonbonded pdb=" O LEU R 94 " pdb=" NE2 GLN R 98 " model vdw 2.335 3.120 ... (remaining 59013 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.270 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:5.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 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 : 0.008 0.093 7488 Z= 0.359 Angle : 1.077 17.625 10148 Z= 0.594 Chirality : 0.058 0.266 1171 Planarity : 0.007 0.065 1277 Dihedral : 11.086 75.182 2674 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.75 (0.23), residues: 921 helix: -1.70 (0.20), residues: 414 sheet: -0.85 (0.39), residues: 169 loop : -2.31 (0.27), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 212 TYR 0.032 0.004 TYR R 354 PHE 0.042 0.004 PHE B 180 TRP 0.026 0.004 TRP B 99 HIS 0.028 0.004 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00841 ( 7486) covalent geometry : angle 1.07502 (10144) SS BOND : bond 0.01511 ( 2) SS BOND : angle 3.11116 ( 4) hydrogen bonds : bond 0.16546 ( 417) hydrogen bonds : angle 7.19023 ( 1227) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.276 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 91 LYS cc_start: 0.7132 (mttt) cc_final: 0.6904 (mmmm) REVERT: R 237 ILE cc_start: 0.8094 (mt) cc_final: 0.7813 (mp) REVERT: R 325 MET cc_start: 0.6473 (mmt) cc_final: 0.5754 (pp-130) REVERT: A 6 SER cc_start: 0.6884 (m) cc_final: 0.6495 (p) REVERT: A 208 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7707 (ttp-110) REVERT: A 245 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7593 (tm-30) REVERT: A 280 LYS cc_start: 0.8342 (mppt) cc_final: 0.7870 (mtmt) REVERT: B 12 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7787 (tp30) REVERT: B 175 GLN cc_start: 0.8375 (mm110) cc_final: 0.8051 (mm-40) REVERT: B 264 TYR cc_start: 0.8458 (m-80) cc_final: 0.8162 (m-80) REVERT: C 19 LEU cc_start: 0.8978 (mt) cc_final: 0.8772 (mt) REVERT: C 27 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7970 (mtt-85) outliers start: 0 outliers final: 2 residues processed: 218 average time/residue: 0.4955 time to fit residues: 113.9086 Evaluate side-chains 136 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 HIS R 238 GLN ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN R 320 HIS R 365 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 259 GLN B 268 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.135635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111528 restraints weight = 11056.589| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.63 r_work: 0.3342 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7488 Z= 0.145 Angle : 0.645 9.785 10148 Z= 0.339 Chirality : 0.043 0.157 1171 Planarity : 0.005 0.039 1277 Dihedral : 5.480 51.362 1013 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.01 % Allowed : 15.41 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.26), residues: 921 helix: 0.49 (0.24), residues: 433 sheet: -0.58 (0.38), residues: 158 loop : -1.83 (0.29), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 49 TYR 0.023 0.002 TYR A 290 PHE 0.011 0.001 PHE A 189 TRP 0.020 0.002 TRP B 82 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7486) covalent geometry : angle 0.64384 (10144) SS BOND : bond 0.01653 ( 2) SS BOND : angle 1.96790 ( 4) hydrogen bonds : bond 0.04756 ( 417) hydrogen bonds : angle 5.02921 ( 1227) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 246 ILE cc_start: 0.8156 (mm) cc_final: 0.7925 (mm) REVERT: R 249 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.7054 (tpp) REVERT: R 325 MET cc_start: 0.6492 (mmt) cc_final: 0.5764 (pp-130) REVERT: A 52 GLN cc_start: 0.7171 (mt0) cc_final: 0.6866 (mp10) REVERT: A 208 ARG cc_start: 0.7759 (ttm-80) cc_final: 0.7051 (ttp-110) REVERT: A 269 ASN cc_start: 0.8925 (m110) cc_final: 0.8601 (m110) REVERT: A 280 LYS cc_start: 0.8067 (mppt) cc_final: 0.7612 (mtmm) REVERT: A 310 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8288 (tt) REVERT: A 318 GLU cc_start: 0.8257 (pm20) cc_final: 0.7446 (pp20) REVERT: B 12 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7767 (tp30) REVERT: B 150 ARG cc_start: 0.7985 (mmt180) cc_final: 0.7758 (mmt180) REVERT: B 175 GLN cc_start: 0.8529 (mm110) cc_final: 0.8085 (mm-40) REVERT: B 217 MET cc_start: 0.8045 (pmm) cc_final: 0.7748 (pmm) REVERT: B 264 TYR cc_start: 0.8678 (m-80) cc_final: 0.8407 (m-80) outliers start: 32 outliers final: 10 residues processed: 165 average time/residue: 0.4668 time to fit residues: 81.4067 Evaluate side-chains 128 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 65 optimal weight: 0.0770 chunk 69 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 GLN ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 304 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106314 restraints weight = 10960.211| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.54 r_work: 0.3262 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7488 Z= 0.205 Angle : 0.656 10.417 10148 Z= 0.343 Chirality : 0.044 0.167 1171 Planarity : 0.005 0.058 1277 Dihedral : 5.271 50.095 1013 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.01 % Allowed : 17.42 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.27), residues: 921 helix: 1.15 (0.24), residues: 432 sheet: -0.51 (0.38), residues: 163 loop : -1.62 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 96 TYR 0.020 0.002 TYR R 339 PHE 0.016 0.002 PHE R 345 TRP 0.024 0.002 TRP B 82 HIS 0.014 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 7486) covalent geometry : angle 0.65525 (10144) SS BOND : bond 0.01142 ( 2) SS BOND : angle 1.80683 ( 4) hydrogen bonds : bond 0.04747 ( 417) hydrogen bonds : angle 4.91779 ( 1227) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 325 MET cc_start: 0.6439 (mmt) cc_final: 0.5817 (pp-130) REVERT: A 52 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6942 (mp10) REVERT: A 269 ASN cc_start: 0.8923 (m110) cc_final: 0.8628 (m110) REVERT: A 280 LYS cc_start: 0.8204 (mppt) cc_final: 0.7806 (mppt) REVERT: A 281 SER cc_start: 0.8329 (OUTLIER) cc_final: 0.7832 (p) REVERT: A 293 SER cc_start: 0.7658 (t) cc_final: 0.7416 (p) REVERT: A 310 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8400 (tt) REVERT: A 318 GLU cc_start: 0.8268 (pm20) cc_final: 0.8032 (pm20) REVERT: B 12 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7677 (tp30) REVERT: B 23 LYS cc_start: 0.7557 (tppp) cc_final: 0.7226 (tptp) REVERT: B 175 GLN cc_start: 0.8594 (mm110) cc_final: 0.8089 (mm-40) REVERT: B 217 MET cc_start: 0.7973 (pmm) cc_final: 0.7675 (pmm) outliers start: 40 outliers final: 18 residues processed: 143 average time/residue: 0.4916 time to fit residues: 74.4099 Evaluate side-chains 132 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 30 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 75 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.105973 restraints weight = 11233.592| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.60 r_work: 0.3265 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7488 Z= 0.175 Angle : 0.625 11.529 10148 Z= 0.326 Chirality : 0.043 0.163 1171 Planarity : 0.004 0.061 1277 Dihedral : 5.018 48.264 1011 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.51 % Allowed : 17.92 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.27), residues: 921 helix: 1.47 (0.25), residues: 432 sheet: -0.25 (0.39), residues: 158 loop : -1.53 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 96 TYR 0.017 0.002 TYR R 339 PHE 0.012 0.001 PHE R 345 TRP 0.020 0.002 TRP B 82 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 7486) covalent geometry : angle 0.62468 (10144) SS BOND : bond 0.00910 ( 2) SS BOND : angle 1.47304 ( 4) hydrogen bonds : bond 0.04496 ( 417) hydrogen bonds : angle 4.81439 ( 1227) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 243 MET cc_start: 0.5849 (OUTLIER) cc_final: 0.5538 (ttm) REVERT: R 249 MET cc_start: 0.7391 (mmm) cc_final: 0.7158 (tpp) REVERT: R 325 MET cc_start: 0.6389 (mmt) cc_final: 0.5837 (pp-130) REVERT: A 52 GLN cc_start: 0.7211 (mt0) cc_final: 0.6863 (mp10) REVERT: A 269 ASN cc_start: 0.8910 (m110) cc_final: 0.8608 (m110) REVERT: A 280 LYS cc_start: 0.8186 (mppt) cc_final: 0.7818 (mppt) REVERT: A 281 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.7775 (p) REVERT: A 293 SER cc_start: 0.7593 (t) cc_final: 0.7335 (p) REVERT: A 310 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8493 (tt) REVERT: A 318 GLU cc_start: 0.8317 (pm20) cc_final: 0.8072 (pm20) REVERT: B 12 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7633 (tp30) REVERT: B 23 LYS cc_start: 0.7667 (tppp) cc_final: 0.7264 (tptp) REVERT: B 154 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8554 (m-30) REVERT: B 175 GLN cc_start: 0.8563 (mm110) cc_final: 0.8072 (mm110) REVERT: B 217 MET cc_start: 0.7983 (pmm) cc_final: 0.7600 (pmm) REVERT: B 234 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.9044 (m-80) REVERT: B 280 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7506 (ttmt) outliers start: 44 outliers final: 18 residues processed: 145 average time/residue: 0.4830 time to fit residues: 74.0404 Evaluate side-chains 133 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 80 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.131559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107277 restraints weight = 10912.341| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.59 r_work: 0.3280 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7488 Z= 0.146 Angle : 0.590 9.685 10148 Z= 0.308 Chirality : 0.042 0.161 1171 Planarity : 0.004 0.062 1277 Dihedral : 4.795 47.122 1011 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.39 % Allowed : 19.17 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.28), residues: 921 helix: 1.85 (0.25), residues: 426 sheet: -0.30 (0.38), residues: 164 loop : -1.47 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 96 TYR 0.017 0.002 TYR R 339 PHE 0.009 0.001 PHE R 345 TRP 0.018 0.002 TRP R 316 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 7486) covalent geometry : angle 0.58951 (10144) SS BOND : bond 0.00685 ( 2) SS BOND : angle 1.12709 ( 4) hydrogen bonds : bond 0.04245 ( 417) hydrogen bonds : angle 4.67149 ( 1227) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 243 MET cc_start: 0.5844 (OUTLIER) cc_final: 0.5502 (ttm) REVERT: R 249 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6991 (tpp) REVERT: R 325 MET cc_start: 0.6316 (mmt) cc_final: 0.5867 (pp-130) REVERT: A 48 THR cc_start: 0.8831 (m) cc_final: 0.8388 (t) REVERT: A 269 ASN cc_start: 0.8922 (m110) cc_final: 0.8709 (m110) REVERT: A 280 LYS cc_start: 0.8206 (mppt) cc_final: 0.7839 (mppt) REVERT: A 281 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.7767 (p) REVERT: A 310 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8600 (tt) REVERT: A 318 GLU cc_start: 0.8367 (pm20) cc_final: 0.8093 (pm20) REVERT: B 12 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7657 (tp30) REVERT: B 175 GLN cc_start: 0.8547 (mm110) cc_final: 0.8071 (mm-40) REVERT: B 217 MET cc_start: 0.7966 (pmm) cc_final: 0.7641 (pmm) REVERT: B 234 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.9009 (m-80) REVERT: B 280 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7396 (ttmt) outliers start: 43 outliers final: 18 residues processed: 147 average time/residue: 0.4637 time to fit residues: 72.2437 Evaluate side-chains 133 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099335 restraints weight = 11270.515| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.51 r_work: 0.3154 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 7488 Z= 0.314 Angle : 0.744 13.030 10148 Z= 0.387 Chirality : 0.048 0.184 1171 Planarity : 0.005 0.067 1277 Dihedral : 5.150 48.556 1009 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 6.64 % Allowed : 19.80 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.27), residues: 921 helix: 1.44 (0.24), residues: 427 sheet: -0.57 (0.38), residues: 168 loop : -1.41 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 96 TYR 0.023 0.003 TYR B 85 PHE 0.020 0.002 PHE R 345 TRP 0.022 0.002 TRP R 316 HIS 0.007 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00744 ( 7486) covalent geometry : angle 0.74353 (10144) SS BOND : bond 0.01157 ( 2) SS BOND : angle 1.79828 ( 4) hydrogen bonds : bond 0.05125 ( 417) hydrogen bonds : angle 5.02400 ( 1227) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 117 time to evaluate : 0.233 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 153 TYR cc_start: 0.8664 (m-80) cc_final: 0.8391 (m-80) REVERT: R 243 MET cc_start: 0.6341 (OUTLIER) cc_final: 0.5853 (tpp) REVERT: R 249 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7271 (mmm) REVERT: R 325 MET cc_start: 0.6529 (mmt) cc_final: 0.5862 (pp-130) REVERT: A 9 ASP cc_start: 0.7983 (t0) cc_final: 0.7633 (t70) REVERT: A 15 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7679 (ttt180) REVERT: A 52 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6518 (mp10) REVERT: A 269 ASN cc_start: 0.9014 (m110) cc_final: 0.8702 (m110) REVERT: A 280 LYS cc_start: 0.8351 (mppt) cc_final: 0.8069 (mppt) REVERT: A 281 SER cc_start: 0.8071 (OUTLIER) cc_final: 0.7564 (p) REVERT: A 310 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8319 (tt) REVERT: A 313 ARG cc_start: 0.7617 (ptp-110) cc_final: 0.7409 (ptp-110) REVERT: A 318 GLU cc_start: 0.8494 (pm20) cc_final: 0.8166 (pm20) REVERT: B 12 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7642 (tp30) REVERT: B 154 ASP cc_start: 0.8996 (OUTLIER) cc_final: 0.8789 (m-30) REVERT: B 175 GLN cc_start: 0.8682 (mm110) cc_final: 0.8200 (mm-40) REVERT: B 217 MET cc_start: 0.7823 (pmm) cc_final: 0.7499 (pmm) REVERT: B 234 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.9027 (m-80) REVERT: B 280 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7317 (ttmt) outliers start: 53 outliers final: 26 residues processed: 151 average time/residue: 0.4851 time to fit residues: 77.7274 Evaluate side-chains 144 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 278 THR Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106295 restraints weight = 10952.054| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.49 r_work: 0.3235 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7488 Z= 0.143 Angle : 0.611 9.882 10148 Z= 0.317 Chirality : 0.042 0.166 1171 Planarity : 0.005 0.071 1277 Dihedral : 4.751 46.043 1009 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.39 % Allowed : 21.80 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.28), residues: 921 helix: 1.95 (0.25), residues: 422 sheet: -0.33 (0.38), residues: 162 loop : -1.57 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 96 TYR 0.018 0.002 TYR R 339 PHE 0.021 0.001 PHE R 242 TRP 0.019 0.002 TRP R 316 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7486) covalent geometry : angle 0.61050 (10144) SS BOND : bond 0.00606 ( 2) SS BOND : angle 1.05308 ( 4) hydrogen bonds : bond 0.04294 ( 417) hydrogen bonds : angle 4.72422 ( 1227) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 0.296 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 123 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8400 (tm-30) REVERT: R 222 LEU cc_start: 0.7589 (mm) cc_final: 0.7208 (mm) REVERT: R 243 MET cc_start: 0.6052 (OUTLIER) cc_final: 0.5648 (ttm) REVERT: R 325 MET cc_start: 0.6277 (mmt) cc_final: 0.5720 (pp-130) REVERT: A 52 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6550 (mp10) REVERT: A 269 ASN cc_start: 0.8964 (m110) cc_final: 0.8621 (m110) REVERT: A 280 LYS cc_start: 0.8250 (mppt) cc_final: 0.7942 (mppt) REVERT: A 281 SER cc_start: 0.8143 (OUTLIER) cc_final: 0.7589 (p) REVERT: A 310 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8601 (tt) REVERT: A 318 GLU cc_start: 0.8358 (pm20) cc_final: 0.8044 (pm20) REVERT: B 12 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7617 (tp30) REVERT: B 175 GLN cc_start: 0.8523 (mm110) cc_final: 0.8031 (mm-40) REVERT: B 217 MET cc_start: 0.7793 (pmm) cc_final: 0.7463 (pmm) REVERT: B 234 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8955 (m-80) REVERT: B 280 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7264 (ttmt) REVERT: C 18 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7697 (mm-40) outliers start: 43 outliers final: 24 residues processed: 151 average time/residue: 0.5214 time to fit residues: 83.3500 Evaluate side-chains 147 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 278 THR Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 56 optimal weight: 0.0040 chunk 39 optimal weight: 0.3980 chunk 75 optimal weight: 0.0270 overall best weight: 0.3250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.133506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109677 restraints weight = 11066.056| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.57 r_work: 0.3300 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7488 Z= 0.121 Angle : 0.592 8.775 10148 Z= 0.306 Chirality : 0.041 0.163 1171 Planarity : 0.005 0.074 1277 Dihedral : 4.531 44.797 1009 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.26 % Allowed : 24.81 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.28), residues: 921 helix: 2.15 (0.25), residues: 426 sheet: -0.33 (0.37), residues: 167 loop : -1.44 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 96 TYR 0.039 0.002 TYR A 290 PHE 0.022 0.001 PHE R 242 TRP 0.017 0.001 TRP R 334 HIS 0.004 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7486) covalent geometry : angle 0.59224 (10144) SS BOND : bond 0.01736 ( 2) SS BOND : angle 0.88494 ( 4) hydrogen bonds : bond 0.03974 ( 417) hydrogen bonds : angle 4.57330 ( 1227) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.217 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 222 LEU cc_start: 0.7564 (mm) cc_final: 0.7190 (mm) REVERT: R 238 GLN cc_start: 0.7571 (mt0) cc_final: 0.7341 (mt0) REVERT: R 325 MET cc_start: 0.6078 (mmt) cc_final: 0.5626 (pp-130) REVERT: A 52 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6579 (mp10) REVERT: A 248 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7957 (mtpp) REVERT: A 269 ASN cc_start: 0.8887 (m110) cc_final: 0.8612 (m110) REVERT: A 280 LYS cc_start: 0.8183 (mppt) cc_final: 0.7797 (mppt) REVERT: A 318 GLU cc_start: 0.8336 (pm20) cc_final: 0.8071 (pm20) REVERT: B 12 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7506 (tp30) REVERT: B 175 GLN cc_start: 0.8491 (mm110) cc_final: 0.8014 (mm-40) REVERT: B 217 MET cc_start: 0.7803 (pmm) cc_final: 0.7502 (pmm) REVERT: B 234 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8233 (t80) REVERT: C 18 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7611 (mm-40) REVERT: C 20 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8532 (mtmm) REVERT: C 21 MET cc_start: 0.8110 (tmt) cc_final: 0.7742 (tmt) outliers start: 26 outliers final: 11 residues processed: 149 average time/residue: 0.4935 time to fit residues: 77.7309 Evaluate side-chains 126 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 256 ASN A 304 GLN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.129610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105760 restraints weight = 10963.522| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.49 r_work: 0.3245 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7488 Z= 0.163 Angle : 0.648 13.669 10148 Z= 0.330 Chirality : 0.043 0.162 1171 Planarity : 0.005 0.083 1277 Dihedral : 4.716 47.588 1009 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.01 % Allowed : 25.19 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.28), residues: 921 helix: 2.08 (0.25), residues: 426 sheet: -0.44 (0.37), residues: 169 loop : -1.43 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 96 TYR 0.019 0.002 TYR R 339 PHE 0.017 0.002 PHE R 242 TRP 0.022 0.002 TRP R 334 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 7486) covalent geometry : angle 0.64799 (10144) SS BOND : bond 0.01052 ( 2) SS BOND : angle 0.90677 ( 4) hydrogen bonds : bond 0.04238 ( 417) hydrogen bonds : angle 4.62990 ( 1227) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.201 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 222 LEU cc_start: 0.7698 (mm) cc_final: 0.7329 (mm) REVERT: R 238 GLN cc_start: 0.7654 (mt0) cc_final: 0.7430 (mt0) REVERT: R 325 MET cc_start: 0.6249 (mmt) cc_final: 0.5590 (pp-130) REVERT: A 52 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6562 (mp10) REVERT: A 269 ASN cc_start: 0.8952 (m110) cc_final: 0.8683 (m110) REVERT: A 280 LYS cc_start: 0.8233 (mppt) cc_final: 0.7893 (mppt) REVERT: A 318 GLU cc_start: 0.8338 (pm20) cc_final: 0.8054 (pm20) REVERT: B 12 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7507 (tp30) REVERT: B 175 GLN cc_start: 0.8507 (mm110) cc_final: 0.8017 (mm-40) REVERT: B 217 MET cc_start: 0.7838 (pmm) cc_final: 0.7567 (pmm) REVERT: B 234 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8983 (m-80) REVERT: C 18 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7722 (mm-40) outliers start: 24 outliers final: 16 residues processed: 133 average time/residue: 0.4661 time to fit residues: 65.6318 Evaluate side-chains 131 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 90 optimal weight: 0.0270 chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 87 optimal weight: 0.0770 chunk 15 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.140427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.117018 restraints weight = 10665.296| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.47 r_work: 0.3508 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7488 Z= 0.122 Angle : 0.631 12.294 10148 Z= 0.318 Chirality : 0.042 0.164 1171 Planarity : 0.005 0.082 1277 Dihedral : 4.544 45.108 1009 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.13 % Allowed : 26.44 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.28), residues: 921 helix: 2.18 (0.25), residues: 426 sheet: -0.13 (0.38), residues: 162 loop : -1.50 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 96 TYR 0.039 0.002 TYR A 290 PHE 0.019 0.001 PHE R 242 TRP 0.026 0.001 TRP R 334 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7486) covalent geometry : angle 0.63105 (10144) SS BOND : bond 0.00674 ( 2) SS BOND : angle 0.89346 ( 4) hydrogen bonds : bond 0.03941 ( 417) hydrogen bonds : angle 4.53462 ( 1227) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.280 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 222 LEU cc_start: 0.7712 (mm) cc_final: 0.7367 (mm) REVERT: R 325 MET cc_start: 0.6308 (mmt) cc_final: 0.5789 (pp-130) REVERT: A 52 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.7034 (mp10) REVERT: A 280 LYS cc_start: 0.8337 (mppt) cc_final: 0.7980 (mppt) REVERT: B 12 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7550 (tp30) REVERT: B 175 GLN cc_start: 0.8486 (mm110) cc_final: 0.8114 (mm-40) REVERT: B 217 MET cc_start: 0.7996 (pmm) cc_final: 0.7771 (pmm) REVERT: B 234 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8398 (t80) REVERT: C 18 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7826 (mm-40) REVERT: C 20 LYS cc_start: 0.9111 (ttmt) cc_final: 0.8663 (mtmm) REVERT: C 21 MET cc_start: 0.8078 (tmt) cc_final: 0.7692 (tmt) outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 0.4767 time to fit residues: 68.1141 Evaluate side-chains 128 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 0.0770 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.137686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.114331 restraints weight = 10703.644| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.41 r_work: 0.3483 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7488 Z= 0.154 Angle : 0.663 13.224 10148 Z= 0.335 Chirality : 0.043 0.176 1171 Planarity : 0.005 0.087 1277 Dihedral : 4.630 46.348 1009 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.51 % Allowed : 25.56 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.28), residues: 921 helix: 2.14 (0.25), residues: 420 sheet: -0.33 (0.38), residues: 169 loop : -1.39 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 96 TYR 0.017 0.002 TYR R 339 PHE 0.017 0.001 PHE R 242 TRP 0.049 0.002 TRP R 334 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7486) covalent geometry : angle 0.66265 (10144) SS BOND : bond 0.01007 ( 2) SS BOND : angle 0.83601 ( 4) hydrogen bonds : bond 0.04106 ( 417) hydrogen bonds : angle 4.58832 ( 1227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2307.37 seconds wall clock time: 40 minutes 2.45 seconds (2402.45 seconds total)