Starting phenix.real_space_refine on Thu Jul 2 10:59:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xp6_33366/07_2026/7xp6_33366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xp6_33366/07_2026/7xp6_33366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xp6_33366/07_2026/7xp6_33366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xp6_33366/07_2026/7xp6_33366.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xp6_33366/07_2026/7xp6_33366.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xp6_33366/07_2026/7xp6_33366.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xp6_33366/07_2026/7xp6_33366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xp6_33366/07_2026/7xp6_33366.map" } resolution = 3.01 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5322 2.51 5 N 1436 2.21 5 O 1531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1964 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 981 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2305 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain breaks: 1 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.57, per 1000 atoms: 0.19 Number of scatterers: 8336 At special positions: 0 Unit cell: (79.04, 101.92, 131.04, 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 47 16.00 O 1531 8.00 N 1436 7.00 C 5322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.04 Simple disulfide: pdb=" SG CYS N 100 " - pdb=" SG CYS N 108 " 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: 0.51 Conformation dependent library (CDL) restraints added in 325.1 milliseconds 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 45.9% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 5 through 36 removed outlier: 3.675A pdb=" N ARG A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 61 removed outlier: 3.656A pdb=" N LEU A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS A 60 " --> pdb=" O MET A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.706A pdb=" N ASN A 104 " --> pdb=" O GLN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 133 removed outlier: 4.184A pdb=" N GLN A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.150A pdb=" N TYR A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 171 removed outlier: 3.743A pdb=" N ALA A 171 " --> pdb=" O PRO A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 186 through 207 removed outlier: 4.229A pdb=" N SER A 207 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 247 removed outlier: 3.771A pdb=" N ASN A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.669A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.803A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 29 through 33 removed outlier: 3.562A pdb=" N TYR N 33 " --> pdb=" O PHE N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 66 Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'R' and resid 4 through 39 Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 76 through 111 removed outlier: 3.760A pdb=" N VAL R 80 " --> pdb=" O ASN R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 124 removed outlier: 3.692A pdb=" N ARG R 124 " --> pdb=" O HIS R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 154 removed outlier: 3.681A pdb=" N VAL R 128 " --> pdb=" O ARG R 124 " (cutoff:3.500A) Proline residue: R 136 - end of helix Processing helix chain 'R' and resid 174 through 213 removed outlier: 3.568A pdb=" N LEU R 182 " --> pdb=" O THR R 178 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL R 186 " --> pdb=" O LEU R 182 " (cutoff:3.500A) Proline residue: R 187 - end of helix removed outlier: 3.680A pdb=" N LEU R 211 " --> pdb=" O LYS R 207 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS R 212 " --> pdb=" O LYS R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 254 Processing helix chain 'R' and resid 258 through 283 removed outlier: 3.745A pdb=" N PHE R 263 " --> pdb=" O PRO R 259 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE R 267 " --> pdb=" O PHE R 263 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA R 268 " --> pdb=" O CYS R 264 " (cutoff:3.500A) Proline residue: R 272 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 283 through 301 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 79 removed outlier: 6.322A pdb=" N HIS A 37 " --> pdb=" O HIS A 85 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE A 87 " --> pdb=" O HIS A 37 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 39 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL A 89 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A 41 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG A 38 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE A 110 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 40 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 112 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU A 42 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ASP A 114 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE A 109 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N PHE A 145 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PHE A 111 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN A 147 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 113 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL A 142 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N HIS A 217 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 144 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.595A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.653A 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: 4.242A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.678A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.426A 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: 6.733A 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: 3.605A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.294A 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: 3.907A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.675A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 12 through 13 removed outlier: 6.888A pdb=" N MET N 35 " --> pdb=" O ASP N 51 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASP N 51 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP N 37 " --> pdb=" O VAL N 49 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1335 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: 1.07 Time building geometry restraints manager: 0.73 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: 2696 1.34 - 1.46: 1999 1.46 - 1.58: 3757 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 8518 Sorted by residual: bond pdb=" CAV SY9 R 501 " pdb=" NAY SY9 R 501 " ideal model delta sigma weight residual 1.454 1.501 -0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" CAG SY9 R 501 " pdb=" CAV SY9 R 501 " ideal model delta sigma weight residual 1.578 1.544 0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" CAX SY9 R 501 " pdb=" NAY SY9 R 501 " ideal model delta sigma weight residual 1.449 1.482 -0.033 2.00e-02 2.50e+03 2.78e+00 bond pdb=" N THR N 112 " pdb=" CA THR N 112 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.50e+00 bond pdb=" CAM SY9 R 501 " pdb=" OAO SY9 R 501 " ideal model delta sigma weight residual 1.411 1.434 -0.023 2.00e-02 2.50e+03 1.35e+00 ... (remaining 8513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11366 2.00 - 4.01: 163 4.01 - 6.01: 18 6.01 - 8.02: 1 8.02 - 10.02: 1 Bond angle restraints: 11549 Sorted by residual: angle pdb=" CA PRO R 187 " pdb=" N PRO R 187 " pdb=" CD PRO R 187 " ideal model delta sigma weight residual 112.00 106.05 5.95 1.40e+00 5.10e-01 1.80e+01 angle pdb=" C GLY A 159 " pdb=" N LYS A 160 " pdb=" CA LYS A 160 " ideal model delta sigma weight residual 121.54 127.94 -6.40 1.91e+00 2.74e-01 1.12e+01 angle pdb=" CB MET R 247 " pdb=" CG MET R 247 " pdb=" SD MET R 247 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CA ARG A 172 " pdb=" CB ARG A 172 " pdb=" CG ARG A 172 " ideal model delta sigma weight residual 114.10 119.64 -5.54 2.00e+00 2.50e-01 7.66e+00 angle pdb=" C ASP B 247 " pdb=" N ALA B 248 " pdb=" CA ALA B 248 " ideal model delta sigma weight residual 122.74 126.63 -3.89 1.44e+00 4.82e-01 7.29e+00 ... (remaining 11544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 4580 15.96 - 31.92: 368 31.92 - 47.88: 80 47.88 - 63.83: 8 63.83 - 79.79: 2 Dihedral angle restraints: 5038 sinusoidal: 1984 harmonic: 3054 Sorted by residual: 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 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA GLY B 185 " pdb=" C GLY B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA PHE N 109 " pdb=" C PHE N 109 " pdb=" N ASP N 110 " pdb=" CA ASP N 110 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1073 0.051 - 0.101: 192 0.101 - 0.152: 42 0.152 - 0.203: 3 0.203 - 0.253: 2 Chirality restraints: 1312 Sorted by residual: chirality pdb=" NAY SY9 R 501 " pdb=" CAS SY9 R 501 " pdb=" CAV SY9 R 501 " pdb=" CAX SY9 R 501 " both_signs ideal model delta sigma weight residual False -2.12 -2.38 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CAK SY9 R 501 " pdb=" CAG SY9 R 501 " pdb=" CAN SY9 R 501 " pdb=" NAH SY9 R 501 " both_signs ideal model delta sigma weight residual False 2.54 2.77 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 1309 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAA SY9 R 501 " 0.233 2.00e-02 2.50e+03 1.59e-01 3.81e+02 pdb=" CAI SY9 R 501 " -0.048 2.00e-02 2.50e+03 pdb=" CAK SY9 R 501 " -0.105 2.00e-02 2.50e+03 pdb=" CAL SY9 R 501 " 0.202 2.00e-02 2.50e+03 pdb=" NAH SY9 R 501 " -0.189 2.00e-02 2.50e+03 pdb=" OAJ SY9 R 501 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 186 " -0.085 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO R 187 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO R 187 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO R 187 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 271 " -0.047 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO R 272 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO R 272 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 272 " -0.040 5.00e-02 4.00e+02 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 120 2.66 - 3.22: 7959 3.22 - 3.78: 12954 3.78 - 4.34: 17208 4.34 - 4.90: 29084 Nonbonded interactions: 67325 Sorted by model distance: nonbonded pdb=" OH TYR A 173 " pdb=" OD2 ASP A 198 " model vdw 2.100 3.040 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.183 3.040 nonbonded pdb=" O ALA A 44 " pdb=" OG SER A 47 " model vdw 2.187 3.040 nonbonded pdb=" OG SER R 103 " pdb=" OG SER R 194 " model vdw 2.200 3.040 nonbonded pdb=" O TYR A 173 " pdb=" NH1 ARG A 191 " model vdw 2.202 3.120 ... (remaining 67320 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.220 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8520 Z= 0.153 Angle : 0.593 10.023 11553 Z= 0.329 Chirality : 0.042 0.253 1312 Planarity : 0.007 0.159 1456 Dihedral : 12.080 79.794 3052 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.26), residues: 1037 helix: 2.57 (0.23), residues: 424 sheet: 0.99 (0.34), residues: 238 loop : -0.33 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.029 0.002 TYR B 59 PHE 0.026 0.001 PHE R 9 TRP 0.014 0.001 TRP A 99 HIS 0.005 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 8518) covalent geometry : angle 0.59273 / 0.33 (11549) SS BOND : bond 0.00307 / 0.16 ( 2) SS BOND : angle 0.69877 / 0.41 ( 4) hydrogen bonds : bond 0.17062 / 11.50 ( 464) hydrogen bonds : angle 6.36902 / 4.64 ( 1335) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 VAL cc_start: 0.8127 (t) cc_final: 0.7919 (t) REVERT: B 8 ARG cc_start: 0.7847 (ttt180) cc_final: 0.7586 (ttt180) REVERT: B 13 GLN cc_start: 0.7979 (tp40) cc_final: 0.7088 (tp40) REVERT: B 45 MET cc_start: 0.8471 (mtp) cc_final: 0.8263 (mtp) REVERT: B 134 ARG cc_start: 0.7572 (ptp-110) cc_final: 0.7261 (ptp90) REVERT: B 264 TYR cc_start: 0.8318 (m-80) cc_final: 0.7988 (m-80) REVERT: B 317 CYS cc_start: 0.6807 (p) cc_final: 0.6541 (p) REVERT: G 19 LEU cc_start: 0.8425 (mm) cc_final: 0.8207 (mm) REVERT: N 14 GLN cc_start: 0.7399 (mm-40) cc_final: 0.7045 (mm-40) REVERT: N 32 ASN cc_start: 0.8571 (m-40) cc_final: 0.8300 (m110) REVERT: N 53 SER cc_start: 0.8060 (t) cc_final: 0.7538 (m) REVERT: R 36 PHE cc_start: 0.7327 (t80) cc_final: 0.7029 (t80) REVERT: R 149 MET cc_start: 0.5481 (tpt) cc_final: 0.5205 (tpt) REVERT: R 181 ILE cc_start: 0.7706 (mm) cc_final: 0.7456 (mm) REVERT: R 193 ILE cc_start: 0.8154 (tp) cc_final: 0.7920 (tp) REVERT: R 222 LYS cc_start: 0.7408 (tmtt) cc_final: 0.7153 (tmtt) REVERT: R 285 LYS cc_start: 0.8465 (pptt) cc_final: 0.8195 (pptt) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.0941 time to fit residues: 28.5352 Evaluate side-chains 225 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 ASN B 44 GLN B 110 ASN B 119 ASN B 155 ASN R 205 HIS R 217 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.146347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.128352 restraints weight = 12533.123| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.22 r_work: 0.3527 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8520 Z= 0.160 Angle : 0.544 5.689 11553 Z= 0.298 Chirality : 0.043 0.198 1312 Planarity : 0.005 0.071 1456 Dihedral : 4.431 23.674 1132 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.65 % Allowed : 8.24 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.26), residues: 1037 helix: 2.80 (0.23), residues: 439 sheet: 0.89 (0.33), residues: 247 loop : -0.46 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 46 TYR 0.025 0.002 TYR B 59 PHE 0.025 0.002 PHE A 87 TRP 0.019 0.002 TRP B 169 HIS 0.006 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 8518) covalent geometry : angle 0.54415 / 0.30 (11549) SS BOND : bond 0.00168 / 0.08 ( 2) SS BOND : angle 1.02513 / 0.53 ( 4) hydrogen bonds : bond 0.04962 / 3.25 ( 464) hydrogen bonds : angle 4.57511 / 3.32 ( 1335) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 249 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8366 (tttt) cc_final: 0.8130 (mttt) REVERT: A 87 PHE cc_start: 0.8214 (p90) cc_final: 0.7941 (p90) REVERT: A 129 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8392 (ttpp) REVERT: A 188 ARG cc_start: 0.8395 (mtm180) cc_final: 0.8056 (mtm-85) REVERT: A 226 ASN cc_start: 0.8481 (m110) cc_final: 0.8109 (m-40) REVERT: B 8 ARG cc_start: 0.8070 (ttt180) cc_final: 0.7748 (ttt180) REVERT: B 13 GLN cc_start: 0.8488 (tp40) cc_final: 0.7585 (tp40) REVERT: B 45 MET cc_start: 0.8810 (mtp) cc_final: 0.8533 (mtp) REVERT: B 119 ASN cc_start: 0.7817 (m-40) cc_final: 0.7595 (m110) REVERT: B 134 ARG cc_start: 0.8253 (ptp-110) cc_final: 0.8010 (ptp90) REVERT: G 19 LEU cc_start: 0.8556 (mm) cc_final: 0.8349 (mm) REVERT: N 14 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7623 (mm110) REVERT: N 32 ASN cc_start: 0.8751 (m-40) cc_final: 0.8531 (m110) REVERT: N 53 SER cc_start: 0.8611 (t) cc_final: 0.8315 (p) REVERT: N 61 TYR cc_start: 0.8521 (m-80) cc_final: 0.8038 (m-80) REVERT: N 121 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7884 (mm-40) REVERT: R 36 PHE cc_start: 0.7860 (t80) cc_final: 0.7611 (t80) REVERT: R 149 MET cc_start: 0.6337 (tpt) cc_final: 0.5990 (tpt) REVERT: R 181 ILE cc_start: 0.7920 (mm) cc_final: 0.7672 (mm) REVERT: R 182 LEU cc_start: 0.8523 (tp) cc_final: 0.8290 (tt) REVERT: R 193 ILE cc_start: 0.8303 (tp) cc_final: 0.8098 (tp) REVERT: R 222 LYS cc_start: 0.7792 (tmtt) cc_final: 0.7492 (tmtt) REVERT: R 280 ILE cc_start: 0.8727 (mt) cc_final: 0.8516 (mm) REVERT: R 285 LYS cc_start: 0.8704 (pptt) cc_final: 0.8477 (pptt) outliers start: 15 outliers final: 13 residues processed: 249 average time/residue: 0.1013 time to fit residues: 32.5652 Evaluate side-chains 254 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 241 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 69 optimal weight: 0.0670 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.0070 chunk 26 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 110 ASN B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.122107 restraints weight = 12435.885| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.16 r_work: 0.3532 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8520 Z= 0.142 Angle : 0.515 7.336 11553 Z= 0.279 Chirality : 0.041 0.189 1312 Planarity : 0.004 0.059 1456 Dihedral : 4.293 21.809 1132 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.31 % Allowed : 10.77 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.26), residues: 1037 helix: 2.86 (0.23), residues: 440 sheet: 0.86 (0.34), residues: 232 loop : -0.45 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.019 0.001 TYR B 59 PHE 0.016 0.001 PHE R 188 TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 8518) covalent geometry : angle 0.51447 / 0.28 (11549) SS BOND : bond 0.00187 / 0.10 ( 2) SS BOND : angle 0.92458 / 0.49 ( 4) hydrogen bonds : bond 0.04478 / 2.92 ( 464) hydrogen bonds : angle 4.31242 / 3.12 ( 1335) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8340 (tttt) cc_final: 0.8113 (mttt) REVERT: A 87 PHE cc_start: 0.8309 (p90) cc_final: 0.8015 (p90) REVERT: A 129 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8403 (ttpp) REVERT: A 169 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7340 (mm-30) REVERT: A 226 ASN cc_start: 0.8421 (m110) cc_final: 0.8076 (m-40) REVERT: B 8 ARG cc_start: 0.8004 (ttt180) cc_final: 0.7735 (ttt180) REVERT: B 13 GLN cc_start: 0.8472 (tp40) cc_final: 0.7573 (tp40) REVERT: B 45 MET cc_start: 0.8805 (mtp) cc_final: 0.8507 (mtp) REVERT: B 119 ASN cc_start: 0.7965 (m-40) cc_final: 0.7601 (m110) REVERT: B 134 ARG cc_start: 0.8246 (ptp-110) cc_final: 0.8031 (ptp90) REVERT: N 14 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7613 (mm110) REVERT: N 32 ASN cc_start: 0.8721 (m-40) cc_final: 0.8488 (m110) REVERT: N 53 SER cc_start: 0.8624 (t) cc_final: 0.8292 (p) REVERT: N 61 TYR cc_start: 0.8492 (m-80) cc_final: 0.8019 (m-80) REVERT: R 36 PHE cc_start: 0.7809 (t80) cc_final: 0.7585 (t80) REVERT: R 149 MET cc_start: 0.6285 (tpt) cc_final: 0.5924 (tpt) REVERT: R 181 ILE cc_start: 0.7967 (mm) cc_final: 0.7704 (mm) REVERT: R 182 LEU cc_start: 0.8496 (tp) cc_final: 0.8268 (tt) REVERT: R 193 ILE cc_start: 0.8268 (tp) cc_final: 0.8047 (tp) REVERT: R 222 LYS cc_start: 0.7781 (tmtt) cc_final: 0.7463 (tmtt) outliers start: 21 outliers final: 16 residues processed: 247 average time/residue: 0.0992 time to fit residues: 31.7212 Evaluate side-chains 261 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 245 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 0.0470 chunk 2 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN B 155 ASN R 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.138993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.121131 restraints weight = 12684.080| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.19 r_work: 0.3517 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8520 Z= 0.158 Angle : 0.510 6.418 11553 Z= 0.277 Chirality : 0.041 0.191 1312 Planarity : 0.004 0.054 1456 Dihedral : 4.292 21.070 1132 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.97 % Allowed : 12.09 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.26), residues: 1037 helix: 2.83 (0.23), residues: 440 sheet: 0.62 (0.33), residues: 236 loop : -0.50 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.018 0.001 TYR B 59 PHE 0.017 0.001 PHE R 188 TRP 0.017 0.002 TRP A 99 HIS 0.003 0.001 HIS R 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 8518) covalent geometry : angle 0.51019 / 0.28 (11549) SS BOND : bond 0.00246 / 0.13 ( 2) SS BOND : angle 0.75556 / 0.40 ( 4) hydrogen bonds : bond 0.04439 / 2.90 ( 464) hydrogen bonds : angle 4.24570 / 3.06 ( 1335) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8333 (tttt) cc_final: 0.8109 (mttt) REVERT: A 29 ASP cc_start: 0.7804 (t0) cc_final: 0.7331 (t0) REVERT: A 87 PHE cc_start: 0.8357 (p90) cc_final: 0.7996 (p90) REVERT: A 122 GLN cc_start: 0.8412 (tp-100) cc_final: 0.8182 (tp-100) REVERT: A 129 LYS cc_start: 0.8737 (ttmm) cc_final: 0.8531 (ttpt) REVERT: A 134 ASN cc_start: 0.7862 (t0) cc_final: 0.7637 (t0) REVERT: A 169 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7306 (mm-30) REVERT: A 226 ASN cc_start: 0.8455 (m110) cc_final: 0.8086 (m-40) REVERT: B 8 ARG cc_start: 0.7992 (ttt180) cc_final: 0.7721 (ttt180) REVERT: B 13 GLN cc_start: 0.8469 (tp40) cc_final: 0.7570 (tp40) REVERT: B 119 ASN cc_start: 0.8019 (m-40) cc_final: 0.7726 (m110) REVERT: B 134 ARG cc_start: 0.8264 (ptp-110) cc_final: 0.8063 (ptp90) REVERT: B 212 ASP cc_start: 0.8159 (t0) cc_final: 0.7854 (t0) REVERT: B 262 MET cc_start: 0.7991 (tpt) cc_final: 0.7769 (tpt) REVERT: N 14 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7652 (mm-40) REVERT: N 32 ASN cc_start: 0.8692 (m-40) cc_final: 0.8459 (m110) REVERT: N 53 SER cc_start: 0.8664 (t) cc_final: 0.8328 (p) REVERT: N 61 TYR cc_start: 0.8517 (m-80) cc_final: 0.8096 (m-80) REVERT: R 26 PHE cc_start: 0.8248 (t80) cc_final: 0.7870 (t80) REVERT: R 36 PHE cc_start: 0.7850 (t80) cc_final: 0.7620 (t80) REVERT: R 149 MET cc_start: 0.6299 (tpt) cc_final: 0.5932 (tpt) REVERT: R 181 ILE cc_start: 0.8026 (mm) cc_final: 0.7786 (mm) REVERT: R 182 LEU cc_start: 0.8545 (tp) cc_final: 0.8342 (tt) REVERT: R 193 ILE cc_start: 0.8316 (tp) cc_final: 0.8111 (tp) REVERT: R 222 LYS cc_start: 0.7797 (tmtt) cc_final: 0.7454 (tmtt) REVERT: R 247 MET cc_start: 0.6595 (mmm) cc_final: 0.6361 (mmm) outliers start: 27 outliers final: 19 residues processed: 261 average time/residue: 0.0920 time to fit residues: 31.5368 Evaluate side-chains 270 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 251 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 0.0470 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN B 155 ASN R 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.138716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.120737 restraints weight = 12688.784| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.21 r_work: 0.3510 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8520 Z= 0.160 Angle : 0.522 5.920 11553 Z= 0.281 Chirality : 0.042 0.203 1312 Planarity : 0.004 0.050 1456 Dihedral : 4.283 20.913 1132 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.30 % Rotamer: Outliers : 3.30 % Allowed : 14.07 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.26), residues: 1037 helix: 2.74 (0.23), residues: 440 sheet: 0.56 (0.32), residues: 232 loop : -0.47 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.016 0.001 TYR B 59 PHE 0.018 0.001 PHE R 188 TRP 0.023 0.002 TRP R 66 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 8518) covalent geometry : angle 0.52201 / 0.28 (11549) SS BOND : bond 0.00230 / 0.12 ( 2) SS BOND : angle 0.71033 / 0.37 ( 4) hydrogen bonds : bond 0.04426 / 2.89 ( 464) hydrogen bonds : angle 4.19378 / 3.03 ( 1335) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 260 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.7394 (mm110) cc_final: 0.7143 (mm110) REVERT: A 15 GLN cc_start: 0.8269 (tt0) cc_final: 0.8015 (tt0) REVERT: A 24 LYS cc_start: 0.8357 (tttt) cc_final: 0.8112 (mttt) REVERT: A 29 ASP cc_start: 0.7832 (t0) cc_final: 0.7362 (t0) REVERT: A 87 PHE cc_start: 0.8401 (p90) cc_final: 0.7995 (p90) REVERT: A 120 ARG cc_start: 0.7986 (mtt180) cc_final: 0.7731 (mtt180) REVERT: A 122 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8152 (tp-100) REVERT: A 129 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8549 (ttpt) REVERT: A 169 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7276 (mm-30) REVERT: A 226 ASN cc_start: 0.8494 (m110) cc_final: 0.8141 (m-40) REVERT: B 8 ARG cc_start: 0.8010 (ttt180) cc_final: 0.7706 (ttt180) REVERT: B 13 GLN cc_start: 0.8525 (tp40) cc_final: 0.7627 (tp40) REVERT: B 61 MET cc_start: 0.7870 (ppp) cc_final: 0.7663 (ppp) REVERT: B 74 SER cc_start: 0.8385 (t) cc_final: 0.8054 (p) REVERT: B 119 ASN cc_start: 0.8062 (m-40) cc_final: 0.7797 (m110) REVERT: B 134 ARG cc_start: 0.8281 (ptp-110) cc_final: 0.8080 (ptp90) REVERT: B 262 MET cc_start: 0.8069 (tpt) cc_final: 0.7867 (tpt) REVERT: N 14 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7644 (mm-40) REVERT: N 32 ASN cc_start: 0.8696 (m-40) cc_final: 0.8471 (m110) REVERT: N 53 SER cc_start: 0.8668 (t) cc_final: 0.8342 (p) REVERT: N 61 TYR cc_start: 0.8552 (m-80) cc_final: 0.8124 (m-80) REVERT: R 26 PHE cc_start: 0.8265 (t80) cc_final: 0.7907 (t80) REVERT: R 36 PHE cc_start: 0.7869 (t80) cc_final: 0.7646 (t80) REVERT: R 149 MET cc_start: 0.6286 (tpt) cc_final: 0.5913 (tpt) REVERT: R 181 ILE cc_start: 0.8055 (mm) cc_final: 0.7843 (mm) REVERT: R 193 ILE cc_start: 0.8292 (tp) cc_final: 0.8087 (tp) REVERT: R 222 LYS cc_start: 0.7808 (tmtt) cc_final: 0.7451 (tmtt) REVERT: R 247 MET cc_start: 0.6623 (mmm) cc_final: 0.6344 (mmm) outliers start: 30 outliers final: 19 residues processed: 265 average time/residue: 0.1030 time to fit residues: 35.7998 Evaluate side-chains 278 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 259 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain N residue 36 ASN Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 56 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 94 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 98 optimal weight: 0.0470 chunk 91 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN B 155 ASN R 31 ASN R 224 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.139460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.121375 restraints weight = 12512.649| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.20 r_work: 0.3517 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8520 Z= 0.135 Angle : 0.514 6.855 11553 Z= 0.274 Chirality : 0.041 0.195 1312 Planarity : 0.004 0.046 1456 Dihedral : 4.195 20.656 1132 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.30 % Rotamer: Outliers : 2.64 % Allowed : 15.16 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.26), residues: 1037 helix: 2.76 (0.23), residues: 440 sheet: 0.54 (0.32), residues: 230 loop : -0.47 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.014 0.001 TYR B 59 PHE 0.018 0.001 PHE R 188 TRP 0.025 0.002 TRP R 66 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 8518) covalent geometry : angle 0.51431 / 0.27 (11549) SS BOND : bond 0.00234 / 0.12 ( 2) SS BOND : angle 0.67336 / 0.35 ( 4) hydrogen bonds : bond 0.04181 / 2.73 ( 464) hydrogen bonds : angle 4.12523 / 2.98 ( 1335) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.7387 (mm110) cc_final: 0.7156 (mm110) REVERT: A 24 LYS cc_start: 0.8346 (tttt) cc_final: 0.8112 (mttt) REVERT: A 29 ASP cc_start: 0.7821 (t0) cc_final: 0.7342 (t0) REVERT: A 87 PHE cc_start: 0.8428 (p90) cc_final: 0.8042 (p90) REVERT: A 120 ARG cc_start: 0.7906 (mtt180) cc_final: 0.7694 (mtt180) REVERT: A 122 GLN cc_start: 0.8420 (tp-100) cc_final: 0.8168 (tp-100) REVERT: A 129 LYS cc_start: 0.8768 (ttmm) cc_final: 0.8559 (ttpt) REVERT: A 134 ASN cc_start: 0.7570 (t0) cc_final: 0.7360 (t0) REVERT: A 135 ARG cc_start: 0.7645 (mmp80) cc_final: 0.6960 (mmp80) REVERT: A 169 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7149 (mm-30) REVERT: A 198 ASP cc_start: 0.7538 (t0) cc_final: 0.7141 (t0) REVERT: A 226 ASN cc_start: 0.8467 (m110) cc_final: 0.8075 (m-40) REVERT: A 240 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8435 (mptt) REVERT: B 8 ARG cc_start: 0.7995 (ttt180) cc_final: 0.7688 (ttt180) REVERT: B 13 GLN cc_start: 0.8521 (tp40) cc_final: 0.7628 (tp40) REVERT: B 74 SER cc_start: 0.8362 (t) cc_final: 0.8047 (p) REVERT: B 119 ASN cc_start: 0.8005 (m-40) cc_final: 0.7761 (m110) REVERT: B 134 ARG cc_start: 0.8320 (ptp-110) cc_final: 0.8085 (ptp90) REVERT: B 204 CYS cc_start: 0.7911 (m) cc_final: 0.7656 (m) REVERT: N 14 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7649 (mm-40) REVERT: N 32 ASN cc_start: 0.8659 (m-40) cc_final: 0.8436 (m110) REVERT: N 53 SER cc_start: 0.8661 (t) cc_final: 0.8334 (p) REVERT: N 61 TYR cc_start: 0.8541 (m-80) cc_final: 0.8103 (m-80) REVERT: R 26 PHE cc_start: 0.8208 (t80) cc_final: 0.7889 (t80) REVERT: R 36 PHE cc_start: 0.7855 (t80) cc_final: 0.7633 (t80) REVERT: R 149 MET cc_start: 0.6326 (tpt) cc_final: 0.5947 (tpt) REVERT: R 181 ILE cc_start: 0.7998 (mm) cc_final: 0.7778 (mm) REVERT: R 193 ILE cc_start: 0.8283 (tp) cc_final: 0.8079 (tp) REVERT: R 222 LYS cc_start: 0.7779 (tmtt) cc_final: 0.7418 (tmtt) REVERT: R 247 MET cc_start: 0.6563 (mmm) cc_final: 0.6223 (mmm) outliers start: 24 outliers final: 22 residues processed: 266 average time/residue: 0.0962 time to fit residues: 33.3548 Evaluate side-chains 278 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain N residue 36 ASN Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 74 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 91 optimal weight: 0.2980 chunk 77 optimal weight: 0.2980 chunk 41 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 155 ASN R 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.139750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.121671 restraints weight = 12756.087| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.22 r_work: 0.3524 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8520 Z= 0.128 Angle : 0.510 6.766 11553 Z= 0.270 Chirality : 0.041 0.195 1312 Planarity : 0.004 0.045 1456 Dihedral : 4.126 20.502 1132 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.01 % Rotamer: Outliers : 2.75 % Allowed : 16.15 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.26), residues: 1037 helix: 2.78 (0.23), residues: 442 sheet: 0.48 (0.32), residues: 232 loop : -0.46 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.015 0.001 TYR B 59 PHE 0.017 0.001 PHE R 188 TRP 0.015 0.002 TRP R 300 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 8518) covalent geometry : angle 0.51003 / 0.27 (11549) SS BOND : bond 0.00249 / 0.13 ( 2) SS BOND : angle 0.60959 / 0.32 ( 4) hydrogen bonds : bond 0.04047 / 2.64 ( 464) hydrogen bonds : angle 4.02241 / 2.92 ( 1335) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.7369 (mm110) cc_final: 0.7128 (mm110) REVERT: A 24 LYS cc_start: 0.8330 (tttt) cc_final: 0.8095 (mttt) REVERT: A 29 ASP cc_start: 0.7814 (t0) cc_final: 0.7331 (t0) REVERT: A 87 PHE cc_start: 0.8484 (p90) cc_final: 0.8049 (p90) REVERT: A 98 LYS cc_start: 0.8152 (mmmt) cc_final: 0.7817 (mmmt) REVERT: A 122 GLN cc_start: 0.8426 (tp-100) cc_final: 0.8193 (tp40) REVERT: A 129 LYS cc_start: 0.8747 (ttmm) cc_final: 0.8543 (ttpt) REVERT: A 135 ARG cc_start: 0.7665 (mmp80) cc_final: 0.7393 (mmp80) REVERT: A 169 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7107 (mm-30) REVERT: A 198 ASP cc_start: 0.7523 (t0) cc_final: 0.7128 (t0) REVERT: A 226 ASN cc_start: 0.8458 (m110) cc_final: 0.8081 (m-40) REVERT: A 236 ASP cc_start: 0.8506 (t0) cc_final: 0.8267 (t70) REVERT: B 8 ARG cc_start: 0.7991 (ttt180) cc_final: 0.7668 (ttt180) REVERT: B 13 GLN cc_start: 0.8510 (tp40) cc_final: 0.7617 (tp40) REVERT: B 74 SER cc_start: 0.8357 (t) cc_final: 0.8036 (p) REVERT: B 119 ASN cc_start: 0.7998 (m-40) cc_final: 0.7766 (m110) REVERT: B 134 ARG cc_start: 0.8311 (ptp-110) cc_final: 0.8083 (ptp90) REVERT: B 204 CYS cc_start: 0.7882 (m) cc_final: 0.7593 (m) REVERT: B 325 MET cc_start: 0.8489 (mmm) cc_final: 0.8277 (mtp) REVERT: N 14 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7628 (mm-40) REVERT: N 32 ASN cc_start: 0.8616 (m-40) cc_final: 0.8406 (m110) REVERT: N 53 SER cc_start: 0.8658 (t) cc_final: 0.8321 (p) REVERT: N 61 TYR cc_start: 0.8546 (m-80) cc_final: 0.8076 (m-80) REVERT: R 26 PHE cc_start: 0.8165 (t80) cc_final: 0.7771 (t80) REVERT: R 36 PHE cc_start: 0.7845 (t80) cc_final: 0.7630 (t80) REVERT: R 106 TYR cc_start: 0.8456 (m-10) cc_final: 0.8248 (m-10) REVERT: R 149 MET cc_start: 0.6233 (tpt) cc_final: 0.5878 (tpt) REVERT: R 181 ILE cc_start: 0.7997 (mm) cc_final: 0.7784 (mm) REVERT: R 222 LYS cc_start: 0.7786 (tmtt) cc_final: 0.7391 (tmtt) REVERT: R 247 MET cc_start: 0.6572 (mmm) cc_final: 0.6240 (mmm) outliers start: 25 outliers final: 21 residues processed: 264 average time/residue: 0.1014 time to fit residues: 34.7346 Evaluate side-chains 277 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 256 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 36 ASN Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 155 ASN ** B 239 ASN ** 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 = 0.3862 r_free = 0.3862 target = 0.138145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.120141 restraints weight = 12421.829| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.17 r_work: 0.3498 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8520 Z= 0.188 Angle : 0.549 6.697 11553 Z= 0.292 Chirality : 0.042 0.185 1312 Planarity : 0.004 0.043 1456 Dihedral : 4.304 20.850 1132 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.09 % Favored : 96.82 % Rotamer: Outliers : 2.97 % Allowed : 16.59 % Favored : 80.44 % 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 are not related in a simple way. whole: 1.61 (0.26), residues: 1037 helix: 2.64 (0.23), residues: 442 sheet: 0.39 (0.32), residues: 232 loop : -0.44 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.017 0.002 TYR B 59 PHE 0.016 0.001 PHE R 188 TRP 0.016 0.002 TRP R 300 HIS 0.004 0.001 HIS R 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 8518) covalent geometry : angle 0.54862 / 0.29 (11549) SS BOND : bond 0.00277 / 0.14 ( 2) SS BOND : angle 0.52076 / 0.28 ( 4) hydrogen bonds : bond 0.04581 / 2.98 ( 464) hydrogen bonds : angle 4.17239 / 3.01 ( 1335) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.7462 (mm110) cc_final: 0.7211 (mm110) REVERT: A 24 LYS cc_start: 0.8353 (tttt) cc_final: 0.8112 (mttt) REVERT: A 29 ASP cc_start: 0.7843 (t0) cc_final: 0.7382 (t0) REVERT: A 87 PHE cc_start: 0.8445 (p90) cc_final: 0.7992 (p90) REVERT: A 122 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8094 (tp-100) REVERT: A 135 ARG cc_start: 0.7597 (mmp80) cc_final: 0.7390 (mmp80) REVERT: A 169 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7058 (mm-30) REVERT: A 198 ASP cc_start: 0.7595 (t0) cc_final: 0.7205 (t0) REVERT: A 226 ASN cc_start: 0.8523 (m110) cc_final: 0.8159 (m-40) REVERT: B 8 ARG cc_start: 0.7983 (ttt180) cc_final: 0.7653 (ttt180) REVERT: B 13 GLN cc_start: 0.8491 (tp40) cc_final: 0.7590 (tp40) REVERT: B 74 SER cc_start: 0.8358 (t) cc_final: 0.8048 (p) REVERT: B 134 ARG cc_start: 0.8277 (ptp-110) cc_final: 0.8067 (ptp90) REVERT: B 204 CYS cc_start: 0.8038 (m) cc_final: 0.7820 (m) REVERT: B 277 SER cc_start: 0.8144 (p) cc_final: 0.7923 (m) REVERT: N 14 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7662 (mm-40) REVERT: N 32 ASN cc_start: 0.8636 (m-40) cc_final: 0.8413 (m110) REVERT: N 53 SER cc_start: 0.8705 (t) cc_final: 0.8342 (p) REVERT: N 61 TYR cc_start: 0.8531 (m-80) cc_final: 0.8063 (m-80) REVERT: N 109 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.6269 (m-80) REVERT: R 26 PHE cc_start: 0.8276 (t80) cc_final: 0.7968 (t80) REVERT: R 36 PHE cc_start: 0.7913 (t80) cc_final: 0.7681 (t80) REVERT: R 149 MET cc_start: 0.6308 (tpt) cc_final: 0.5954 (tpt) REVERT: R 222 LYS cc_start: 0.7934 (tmtt) cc_final: 0.7556 (tmtt) REVERT: R 247 MET cc_start: 0.6547 (mmm) cc_final: 0.6203 (mmm) outliers start: 27 outliers final: 24 residues processed: 259 average time/residue: 0.1150 time to fit residues: 38.7450 Evaluate side-chains 267 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 36 ASN Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 66 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 0.0070 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN ** R 224 HIS ** 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 = 0.3892 r_free = 0.3892 target = 0.144731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126560 restraints weight = 12507.044| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.22 r_work: 0.3506 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8520 Z= 0.136 Angle : 0.529 6.811 11553 Z= 0.279 Chirality : 0.041 0.194 1312 Planarity : 0.004 0.044 1456 Dihedral : 4.170 20.773 1132 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.30 % Rotamer: Outliers : 2.75 % Allowed : 17.03 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.26), residues: 1037 helix: 2.72 (0.23), residues: 442 sheet: 0.42 (0.33), residues: 221 loop : -0.47 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.016 0.001 TYR R 106 PHE 0.017 0.001 PHE R 188 TRP 0.016 0.002 TRP R 300 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 8518) covalent geometry : angle 0.52925 / 0.28 (11549) SS BOND : bond 0.00245 / 0.13 ( 2) SS BOND : angle 0.58751 / 0.34 ( 4) hydrogen bonds : bond 0.04172 / 2.73 ( 464) hydrogen bonds : angle 4.05242 / 2.94 ( 1335) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.7403 (mm110) cc_final: 0.7153 (mm110) REVERT: A 24 LYS cc_start: 0.8353 (tttt) cc_final: 0.8110 (mttt) REVERT: A 29 ASP cc_start: 0.7850 (t0) cc_final: 0.7348 (t0) REVERT: A 87 PHE cc_start: 0.8448 (p90) cc_final: 0.8010 (p90) REVERT: A 122 GLN cc_start: 0.8399 (tp-100) cc_final: 0.8100 (tp-100) REVERT: A 198 ASP cc_start: 0.7552 (t0) cc_final: 0.7187 (t0) REVERT: A 211 ARG cc_start: 0.8286 (mtp85) cc_final: 0.8073 (mtp85) REVERT: A 236 ASP cc_start: 0.8547 (t70) cc_final: 0.8302 (t70) REVERT: A 240 LYS cc_start: 0.8724 (mmtm) cc_final: 0.8439 (mttp) REVERT: B 8 ARG cc_start: 0.8060 (ttt180) cc_final: 0.7718 (ttt180) REVERT: B 13 GLN cc_start: 0.8487 (tp40) cc_final: 0.7590 (tp40) REVERT: B 74 SER cc_start: 0.8365 (t) cc_final: 0.8055 (p) REVERT: B 134 ARG cc_start: 0.8309 (ptp-110) cc_final: 0.8103 (ptp90) REVERT: B 204 CYS cc_start: 0.7928 (m) cc_final: 0.7680 (m) REVERT: B 277 SER cc_start: 0.8135 (p) cc_final: 0.7915 (m) REVERT: N 14 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7756 (mm-40) REVERT: N 32 ASN cc_start: 0.8600 (m-40) cc_final: 0.8397 (m110) REVERT: N 53 SER cc_start: 0.8691 (t) cc_final: 0.8341 (p) REVERT: N 61 TYR cc_start: 0.8542 (m-80) cc_final: 0.8047 (m-80) REVERT: N 109 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: R 26 PHE cc_start: 0.8166 (t80) cc_final: 0.7795 (t80) REVERT: R 36 PHE cc_start: 0.7840 (t80) cc_final: 0.7623 (t80) REVERT: R 106 TYR cc_start: 0.8328 (m-10) cc_final: 0.8054 (m-10) REVERT: R 149 MET cc_start: 0.6235 (tpt) cc_final: 0.5880 (tpt) REVERT: R 222 LYS cc_start: 0.7909 (tmtt) cc_final: 0.7522 (tmtt) REVERT: R 247 MET cc_start: 0.6553 (mmm) cc_final: 0.6170 (mmm) outliers start: 25 outliers final: 23 residues processed: 252 average time/residue: 0.1178 time to fit residues: 38.4674 Evaluate side-chains 264 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 36 ASN Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.0670 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 100 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN R 224 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.139284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.121447 restraints weight = 12539.161| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.19 r_work: 0.3517 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8520 Z= 0.136 Angle : 0.536 6.795 11553 Z= 0.282 Chirality : 0.041 0.194 1312 Planarity : 0.004 0.044 1456 Dihedral : 4.113 20.473 1132 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.01 % Rotamer: Outliers : 2.64 % Allowed : 17.25 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.26), residues: 1037 helix: 2.75 (0.23), residues: 442 sheet: 0.38 (0.33), residues: 214 loop : -0.45 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.015 0.001 TYR B 59 PHE 0.017 0.001 PHE R 188 TRP 0.016 0.002 TRP R 300 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8518) covalent geometry : angle 0.53628 / 0.28 (11549) SS BOND : bond 0.00255 / 0.13 ( 2) SS BOND : angle 0.54584 / 0.31 ( 4) hydrogen bonds : bond 0.04126 / 2.70 ( 464) hydrogen bonds : angle 4.05600 / 2.94 ( 1335) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.7410 (mm110) cc_final: 0.7193 (mm110) REVERT: A 24 LYS cc_start: 0.8340 (tttt) cc_final: 0.8089 (mttt) REVERT: A 29 ASP cc_start: 0.7802 (t0) cc_final: 0.7291 (t0) REVERT: A 87 PHE cc_start: 0.8415 (p90) cc_final: 0.7931 (p90) REVERT: A 122 GLN cc_start: 0.8369 (tp-100) cc_final: 0.8115 (tp40) REVERT: A 198 ASP cc_start: 0.7553 (t0) cc_final: 0.7183 (t0) REVERT: A 211 ARG cc_start: 0.8273 (mtp85) cc_final: 0.8071 (mtp85) REVERT: A 236 ASP cc_start: 0.8514 (t70) cc_final: 0.8067 (t0) REVERT: A 240 LYS cc_start: 0.8701 (mmtm) cc_final: 0.8421 (mttp) REVERT: B 8 ARG cc_start: 0.8036 (ttt180) cc_final: 0.7689 (ttt180) REVERT: B 13 GLN cc_start: 0.8474 (tp40) cc_final: 0.7571 (tp40) REVERT: B 74 SER cc_start: 0.8380 (t) cc_final: 0.8069 (p) REVERT: B 134 ARG cc_start: 0.8270 (ptp-110) cc_final: 0.8028 (ptp90) REVERT: B 204 CYS cc_start: 0.7914 (m) cc_final: 0.7677 (m) REVERT: B 277 SER cc_start: 0.8138 (p) cc_final: 0.7905 (m) REVERT: B 325 MET cc_start: 0.8276 (mtp) cc_final: 0.8059 (mtp) REVERT: N 14 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7728 (mm-40) REVERT: N 53 SER cc_start: 0.8682 (t) cc_final: 0.8323 (p) REVERT: N 61 TYR cc_start: 0.8515 (m-80) cc_final: 0.8057 (m-80) REVERT: N 109 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7446 (m-80) REVERT: R 26 PHE cc_start: 0.8082 (t80) cc_final: 0.7855 (t80) REVERT: R 36 PHE cc_start: 0.7841 (t80) cc_final: 0.7624 (t80) REVERT: R 106 TYR cc_start: 0.8333 (m-10) cc_final: 0.8095 (m-10) REVERT: R 149 MET cc_start: 0.6231 (tpt) cc_final: 0.5872 (tpt) REVERT: R 222 LYS cc_start: 0.7903 (tmtt) cc_final: 0.7515 (tmtt) REVERT: R 247 MET cc_start: 0.6533 (mmm) cc_final: 0.6163 (mmm) outliers start: 24 outliers final: 22 residues processed: 255 average time/residue: 0.1167 time to fit residues: 38.5295 Evaluate side-chains 272 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 249 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 36 ASN Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 90 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN ** R 224 HIS ** 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 = 0.3886 r_free = 0.3886 target = 0.144005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.125742 restraints weight = 12444.914| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.24 r_work: 0.3502 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8520 Z= 0.163 Angle : 0.561 8.820 11553 Z= 0.293 Chirality : 0.042 0.190 1312 Planarity : 0.004 0.044 1456 Dihedral : 4.186 20.706 1132 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.99 % Favored : 96.91 % Rotamer: Outliers : 2.64 % Allowed : 18.24 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.25), residues: 1037 helix: 2.69 (0.23), residues: 441 sheet: 0.36 (0.33), residues: 214 loop : -0.55 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.017 0.002 TYR B 59 PHE 0.017 0.001 PHE R 188 TRP 0.016 0.002 TRP R 300 HIS 0.003 0.001 HIS R 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 8518) covalent geometry : angle 0.56077 / 0.29 (11549) SS BOND : bond 0.00273 / 0.14 ( 2) SS BOND : angle 0.48109 / 0.26 ( 4) hydrogen bonds : bond 0.04326 / 2.81 ( 464) hydrogen bonds : angle 4.07229 / 2.96 ( 1335) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2198.72 seconds wall clock time: 38 minutes 25.64 seconds (2305.64 seconds total)