Starting phenix.real_space_refine on Tue Mar 3 19:55:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xp6_33366/03_2026/7xp6_33366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xp6_33366/03_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_33366/03_2026/7xp6_33366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xp6_33366/03_2026/7xp6_33366.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xp6_33366/03_2026/7xp6_33366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xp6_33366/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.63, per 1000 atoms: 0.20 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: 0.76 Conformation dependent library (CDL) restraints added in 261.9 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: 0.27 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: 1.39 Time building geometry restraints manager: 0.98 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 - 34.38: 5019 34.38 - 68.76: 74 68.76 - 103.14: 2 103.14 - 137.51: 3 137.51 - 171.89: 1 Dihedral angle restraints: 5099 sinusoidal: 2045 harmonic: 3054 Sorted by residual: dihedral pdb=" CAM SY9 R 501 " pdb=" CAP SY9 R 501 " pdb=" OAO SY9 R 501 " pdb=" CAQ SY9 R 501 " ideal model delta sinusoidal sigma weight residual -84.84 87.05 -171.89 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CAR SY9 R 501 " pdb=" CAP SY9 R 501 " pdb=" CAQ SY9 R 501 " pdb=" OAO SY9 R 501 " ideal model delta sinusoidal sigma weight residual 65.89 -56.55 122.44 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 5096 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: 1.110 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: 0.020 Set scattering table: 0.020 Process input model: 8.450 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 : 13.311 171.893 3113 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 covalent geometry : bond 0.00320 ( 8518) covalent geometry : angle 0.59273 (11549) SS BOND : bond 0.00307 ( 2) SS BOND : angle 0.69877 ( 4) hydrogen bonds : bond 0.17062 ( 464) hydrogen bonds : angle 6.36902 ( 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 : 0.300 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: 0.1198 time to fit residues: 35.8597 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 : 0.288 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3906 r_free = 0.3906 target = 0.146405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.128380 restraints weight = 12541.232| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.23 r_work: 0.3525 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1204 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 : 0.546 7.425 11553 Z= 0.298 Chirality : 0.043 0.198 1312 Planarity : 0.005 0.071 1456 Dihedral : 8.268 150.994 1193 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: 1.91 (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 0.006 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 0.005 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8518) covalent geometry : angle 0.54587 (11549) SS BOND : bond 0.00168 ( 2) SS BOND : angle 1.04356 ( 4) hydrogen bonds : bond 0.04926 ( 464) hydrogen bonds : angle 4.57941 ( 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 266 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8350 (tttt) cc_final: 0.8112 (mttt) REVERT: A 87 PHE cc_start: 0.8209 (p90) cc_final: 0.7938 (p90) REVERT: A 129 LYS cc_start: 0.8693 (ttmm) cc_final: 0.8375 (ttpp) REVERT: A 188 ARG cc_start: 0.8389 (mtm180) cc_final: 0.8027 (mtm-85) REVERT: A 226 ASN cc_start: 0.8480 (m110) cc_final: 0.8103 (m-40) REVERT: B 8 ARG cc_start: 0.8087 (ttt180) cc_final: 0.7743 (ttt180) REVERT: B 13 GLN cc_start: 0.8497 (tp40) cc_final: 0.7589 (tp40) REVERT: B 45 MET cc_start: 0.8814 (mtp) cc_final: 0.8537 (mtp) REVERT: B 119 ASN cc_start: 0.7827 (m-40) cc_final: 0.7607 (m110) REVERT: B 134 ARG cc_start: 0.8315 (ptp-110) cc_final: 0.8079 (ptp90) REVERT: G 19 LEU cc_start: 0.8541 (mm) cc_final: 0.8331 (mm) REVERT: N 14 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7623 (mm110) REVERT: N 32 ASN cc_start: 0.8749 (m-40) cc_final: 0.8530 (m110) REVERT: N 53 SER cc_start: 0.8615 (t) cc_final: 0.8307 (p) REVERT: N 61 TYR cc_start: 0.8523 (m-80) cc_final: 0.8046 (m-80) REVERT: N 121 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7874 (mm-40) REVERT: R 36 PHE cc_start: 0.7892 (t80) cc_final: 0.7633 (t80) REVERT: R 149 MET cc_start: 0.6348 (tpt) cc_final: 0.6002 (tpt) REVERT: R 181 ILE cc_start: 0.7925 (mm) cc_final: 0.7672 (mm) REVERT: R 182 LEU cc_start: 0.8528 (tp) cc_final: 0.8294 (tt) REVERT: R 193 ILE cc_start: 0.8305 (tp) cc_final: 0.8097 (tp) REVERT: R 222 LYS cc_start: 0.7800 (tmtt) cc_final: 0.7499 (tmtt) REVERT: R 280 ILE cc_start: 0.8723 (mt) cc_final: 0.8511 (mm) outliers start: 15 outliers final: 13 residues processed: 251 average time/residue: 0.1170 time to fit residues: 37.6236 Evaluate side-chains 257 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 244 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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: 3.9990 chunk 69 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3870 r_free = 0.3870 target = 0.138465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.120779 restraints weight = 12430.644| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.15 r_work: 0.3512 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1568 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= 0.187 Angle : 0.545 8.206 11553 Z= 0.295 Chirality : 0.043 0.188 1312 Planarity : 0.005 0.059 1456 Dihedral : 7.984 145.483 1193 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 2.53 % Allowed : 10.55 % 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: 1.79 (0.26), residues: 1037 helix: 2.73 (0.23), residues: 440 sheet: 0.74 (0.33), residues: 234 loop : -0.47 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.024 0.002 TYR B 59 PHE 0.018 0.001 PHE R 188 TRP 0.019 0.002 TRP R 66 HIS 0.005 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 8518) covalent geometry : angle 0.54506 (11549) SS BOND : bond 0.00206 ( 2) SS BOND : angle 0.91910 ( 4) hydrogen bonds : bond 0.04849 ( 464) hydrogen bonds : angle 4.40404 ( 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 278 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8346 (tttt) cc_final: 0.8117 (mttt) REVERT: A 87 PHE cc_start: 0.8322 (p90) cc_final: 0.8009 (p90) REVERT: A 122 GLN cc_start: 0.8443 (tp-100) cc_final: 0.8177 (tp-100) REVERT: A 129 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8530 (ttpt) REVERT: A 169 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7372 (mm-30) REVERT: A 185 GLU cc_start: 0.6667 (pt0) cc_final: 0.6225 (pt0) REVERT: A 190 THR cc_start: 0.8302 (t) cc_final: 0.7922 (p) REVERT: A 191 ARG cc_start: 0.8256 (ttp80) cc_final: 0.7925 (mtp-110) REVERT: A 226 ASN cc_start: 0.8478 (m110) cc_final: 0.8110 (m-40) REVERT: B 8 ARG cc_start: 0.7978 (ttt180) cc_final: 0.7661 (ttt180) REVERT: B 13 GLN cc_start: 0.8490 (tp40) cc_final: 0.7590 (tp40) REVERT: B 119 ASN cc_start: 0.8079 (m-40) cc_final: 0.7719 (m110) REVERT: B 134 ARG cc_start: 0.8237 (ptp-110) cc_final: 0.8020 (ptp90) REVERT: N 14 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7579 (mm-40) REVERT: N 32 ASN cc_start: 0.8745 (m-40) cc_final: 0.8515 (m110) REVERT: N 53 SER cc_start: 0.8644 (t) cc_final: 0.8335 (p) REVERT: N 61 TYR cc_start: 0.8516 (m-80) cc_final: 0.8074 (m-80) REVERT: N 121 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7924 (mm-40) REVERT: R 36 PHE cc_start: 0.7874 (t80) cc_final: 0.7638 (t80) REVERT: R 149 MET cc_start: 0.6288 (tpt) cc_final: 0.5956 (tpt) REVERT: R 181 ILE cc_start: 0.8029 (mm) cc_final: 0.7791 (mm) REVERT: R 182 LEU cc_start: 0.8543 (tp) cc_final: 0.8326 (tt) REVERT: R 193 ILE cc_start: 0.8288 (tp) cc_final: 0.8076 (tp) REVERT: R 222 LYS cc_start: 0.7868 (tmtt) cc_final: 0.7548 (tmtt) outliers start: 23 outliers final: 18 residues processed: 258 average time/residue: 0.1172 time to fit residues: 38.8079 Evaluate side-chains 273 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 27 ILE 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 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: 0.9990 chunk 48 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 88 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 = 0.3881 r_free = 0.3881 target = 0.139561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.121627 restraints weight = 12696.415| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.20 r_work: 0.3521 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8520 Z= 0.132 Angle : 0.509 10.757 11553 Z= 0.271 Chirality : 0.041 0.160 1312 Planarity : 0.004 0.053 1456 Dihedral : 6.791 129.492 1193 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.51 % Favored : 97.40 % Rotamer: Outliers : 2.97 % Allowed : 12.75 % Favored : 84.29 % 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: 1.81 (0.26), residues: 1037 helix: 2.83 (0.23), residues: 440 sheet: 0.61 (0.33), residues: 234 loop : -0.46 (0.31), 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 0.018 0.001 PHE R 188 TRP 0.017 0.002 TRP B 169 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8518) covalent geometry : angle 0.50911 (11549) SS BOND : bond 0.00237 ( 2) SS BOND : angle 0.79118 ( 4) hydrogen bonds : bond 0.04245 ( 464) hydrogen bonds : angle 4.19497 ( 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 286 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 259 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.7387 (mm110) cc_final: 0.7146 (mm110) REVERT: A 24 LYS cc_start: 0.8340 (tttt) cc_final: 0.8101 (mttt) REVERT: A 29 ASP cc_start: 0.7815 (t0) cc_final: 0.7348 (t0) REVERT: A 87 PHE cc_start: 0.8361 (p90) cc_final: 0.8005 (p90) REVERT: A 122 GLN cc_start: 0.8404 (tp-100) cc_final: 0.8162 (tp-100) REVERT: A 129 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8516 (ttpt) REVERT: A 169 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7276 (mm-30) REVERT: A 226 ASN cc_start: 0.8459 (m110) cc_final: 0.8098 (m-40) REVERT: B 8 ARG cc_start: 0.7996 (ttt180) cc_final: 0.7721 (ttt180) REVERT: B 13 GLN cc_start: 0.8483 (tp40) cc_final: 0.7581 (tp40) REVERT: B 74 SER cc_start: 0.8379 (t) cc_final: 0.8098 (m) REVERT: B 119 ASN cc_start: 0.7992 (m-40) cc_final: 0.7713 (m110) REVERT: B 134 ARG cc_start: 0.8289 (ptp-110) cc_final: 0.8084 (ptp90) REVERT: B 212 ASP cc_start: 0.8171 (t0) cc_final: 0.7835 (t0) REVERT: B 262 MET cc_start: 0.7992 (tpt) cc_final: 0.7773 (tpt) REVERT: N 14 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7611 (mm-40) REVERT: N 32 ASN cc_start: 0.8712 (m-40) cc_final: 0.8485 (m110) REVERT: N 53 SER cc_start: 0.8660 (t) cc_final: 0.8300 (p) REVERT: N 61 TYR cc_start: 0.8539 (m-80) cc_final: 0.8113 (m-80) REVERT: R 26 PHE cc_start: 0.8198 (t80) cc_final: 0.7867 (t80) REVERT: R 36 PHE cc_start: 0.7834 (t80) cc_final: 0.7608 (t80) REVERT: R 149 MET cc_start: 0.6273 (tpt) cc_final: 0.5909 (tpt) REVERT: R 181 ILE cc_start: 0.8018 (mm) cc_final: 0.7761 (mm) REVERT: R 182 LEU cc_start: 0.8544 (tp) cc_final: 0.8328 (tt) REVERT: R 193 ILE cc_start: 0.8296 (tp) cc_final: 0.8086 (tp) REVERT: R 222 LYS cc_start: 0.7742 (tmtt) cc_final: 0.7401 (tmtt) REVERT: R 247 MET cc_start: 0.6621 (mmm) cc_final: 0.6384 (mmm) outliers start: 27 outliers final: 18 residues processed: 267 average time/residue: 0.1143 time to fit residues: 39.1747 Evaluate side-chains 272 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 254 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 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 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: 0.3980 chunk 39 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 134 ASN B 88 ASN B 155 ASN R 31 ASN ** R 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.139407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.121308 restraints weight = 12656.651| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.21 r_work: 0.3520 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1913 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= 0.140 Angle : 0.507 6.214 11553 Z= 0.273 Chirality : 0.041 0.199 1312 Planarity : 0.004 0.050 1456 Dihedral : 4.167 20.311 1193 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.70 % Favored : 97.20 % Rotamer: Outliers : 3.30 % Allowed : 14.40 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.76 (0.26), residues: 1037 helix: 2.81 (0.23), residues: 440 sheet: 0.56 (0.33), residues: 232 loop : -0.49 (0.31), residues: 365 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 0.018 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 covalent geometry : bond 0.00306 ( 8518) covalent geometry : angle 0.50709 (11549) SS BOND : bond 0.00231 ( 2) SS BOND : angle 0.66838 ( 4) hydrogen bonds : bond 0.04245 ( 464) hydrogen bonds : angle 4.15188 ( 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 284 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 0.372 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: 0.7175 (mm110) REVERT: A 24 LYS cc_start: 0.8337 (tttt) cc_final: 0.8089 (mttt) REVERT: A 29 ASP cc_start: 0.7829 (t0) cc_final: 0.7343 (t0) REVERT: A 87 PHE cc_start: 0.8415 (p90) cc_final: 0.8067 (p90) REVERT: A 120 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7708 (mtm180) REVERT: A 122 GLN cc_start: 0.8387 (tp-100) cc_final: 0.8139 (tp-100) REVERT: A 129 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8520 (ttpt) REVERT: A 169 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7187 (mm-30) REVERT: A 198 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7095 (t0) REVERT: A 226 ASN cc_start: 0.8457 (m110) cc_final: 0.8098 (m-40) REVERT: B 8 ARG cc_start: 0.7990 (ttt180) cc_final: 0.7686 (ttt180) REVERT: B 13 GLN cc_start: 0.8512 (tp40) cc_final: 0.7612 (tp40) REVERT: B 74 SER cc_start: 0.8365 (t) cc_final: 0.8126 (m) REVERT: B 134 ARG cc_start: 0.8279 (ptp-110) cc_final: 0.8076 (ptp90) REVERT: B 262 MET cc_start: 0.8091 (tpt) cc_final: 0.7845 (tpt) REVERT: N 14 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7660 (mm-40) REVERT: N 32 ASN cc_start: 0.8690 (m-40) cc_final: 0.8464 (m110) REVERT: N 53 SER cc_start: 0.8655 (t) cc_final: 0.8299 (p) REVERT: N 61 TYR cc_start: 0.8539 (m-80) cc_final: 0.8048 (m-80) REVERT: R 26 PHE cc_start: 0.8192 (t80) cc_final: 0.7883 (t80) REVERT: R 36 PHE cc_start: 0.7844 (t80) cc_final: 0.7629 (t80) REVERT: R 149 MET cc_start: 0.6339 (tpt) cc_final: 0.5965 (tpt) REVERT: R 181 ILE cc_start: 0.8046 (mm) cc_final: 0.7825 (mm) REVERT: R 182 LEU cc_start: 0.8544 (tp) cc_final: 0.8344 (tt) REVERT: R 193 ILE cc_start: 0.8292 (tp) cc_final: 0.8083 (tp) REVERT: R 222 LYS cc_start: 0.7787 (tmtt) cc_final: 0.7426 (tmtt) REVERT: R 247 MET cc_start: 0.6592 (mmm) cc_final: 0.6323 (mmm) outliers start: 30 outliers final: 20 residues processed: 260 average time/residue: 0.1106 time to fit residues: 37.4260 Evaluate side-chains 275 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 254 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN 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 172 ARG Chi-restraints excluded: chain A residue 198 ASP 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 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 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: 0.9980 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 0.0370 chunk 94 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 6 optimal weight: 0.0010 chunk 59 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 119 ASN B 155 ASN R 31 ASN R 224 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.121928 restraints weight = 12507.721| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.19 r_work: 0.3527 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2056 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= 0.126 Angle : 0.497 6.465 11553 Z= 0.268 Chirality : 0.040 0.151 1312 Planarity : 0.004 0.045 1456 Dihedral : 4.098 19.723 1193 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.70 % Favored : 97.20 % Rotamer: Outliers : 2.86 % Allowed : 14.95 % 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: 1.77 (0.26), residues: 1037 helix: 2.82 (0.23), residues: 440 sheet: 0.59 (0.33), residues: 230 loop : -0.50 (0.31), residues: 367 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 0.018 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 covalent geometry : bond 0.00274 ( 8518) covalent geometry : angle 0.49696 (11549) SS BOND : bond 0.00231 ( 2) SS BOND : angle 0.66206 ( 4) hydrogen bonds : bond 0.04076 ( 464) hydrogen bonds : angle 4.05618 ( 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 288 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 262 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.7383 (mm110) cc_final: 0.7142 (mm110) REVERT: A 24 LYS cc_start: 0.8325 (tttt) cc_final: 0.8083 (mttt) REVERT: A 29 ASP cc_start: 0.7774 (t0) cc_final: 0.7285 (t0) REVERT: A 87 PHE cc_start: 0.8456 (p90) cc_final: 0.8075 (p90) REVERT: A 120 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7674 (mtt180) REVERT: A 169 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7144 (mm-30) REVERT: A 198 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7104 (t0) REVERT: A 226 ASN cc_start: 0.8434 (m110) cc_final: 0.8060 (m-40) REVERT: A 240 LYS cc_start: 0.8773 (mmtm) cc_final: 0.8439 (mptt) REVERT: B 8 ARG cc_start: 0.7998 (ttt180) cc_final: 0.7682 (ttt180) REVERT: B 13 GLN cc_start: 0.8517 (tp40) cc_final: 0.7619 (tp40) REVERT: B 74 SER cc_start: 0.8361 (t) cc_final: 0.8105 (m) REVERT: B 119 ASN cc_start: 0.7775 (m-40) cc_final: 0.7368 (m110) REVERT: B 134 ARG cc_start: 0.8296 (ptp-110) cc_final: 0.8057 (ptp90) REVERT: B 204 CYS cc_start: 0.7919 (m) cc_final: 0.7631 (m) REVERT: N 14 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7639 (mm-40) REVERT: N 32 ASN cc_start: 0.8664 (m-40) cc_final: 0.8452 (m110) REVERT: N 61 TYR cc_start: 0.8538 (m-80) cc_final: 0.8027 (m-80) REVERT: R 26 PHE cc_start: 0.8155 (t80) cc_final: 0.7866 (t80) REVERT: R 36 PHE cc_start: 0.7825 (t80) cc_final: 0.7607 (t80) REVERT: R 149 MET cc_start: 0.6305 (tpt) cc_final: 0.5929 (tpt) REVERT: R 181 ILE cc_start: 0.8025 (mm) cc_final: 0.7799 (mm) REVERT: R 182 LEU cc_start: 0.8520 (tp) cc_final: 0.8305 (tt) REVERT: R 193 ILE cc_start: 0.8265 (tp) cc_final: 0.8060 (tp) REVERT: R 247 MET cc_start: 0.6563 (mmm) cc_final: 0.6234 (mmm) outliers start: 26 outliers final: 21 residues processed: 266 average time/residue: 0.1127 time to fit residues: 38.7487 Evaluate side-chains 274 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 252 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN 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 172 ARG Chi-restraints excluded: chain A residue 198 ASP 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 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: 0.9980 chunk 81 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 77 optimal weight: 0.0970 chunk 41 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 82 optimal weight: 0.0980 chunk 44 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 88 ASN B 155 ASN R 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.140682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.122505 restraints weight = 12723.402| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.22 r_work: 0.3534 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8520 Z= 0.113 Angle : 0.486 6.591 11553 Z= 0.262 Chirality : 0.040 0.147 1312 Planarity : 0.004 0.042 1456 Dihedral : 4.014 18.707 1193 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.75 % Allowed : 16.37 % Favored : 80.88 % 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: 1.82 (0.26), residues: 1037 helix: 2.85 (0.23), residues: 442 sheet: 0.56 (0.33), 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 0.013 0.001 TYR R 241 PHE 0.017 0.001 PHE R 188 TRP 0.017 0.002 TRP R 88 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8518) covalent geometry : angle 0.48635 (11549) SS BOND : bond 0.00218 ( 2) SS BOND : angle 0.62223 ( 4) hydrogen bonds : bond 0.03860 ( 464) hydrogen bonds : angle 3.99422 ( 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 264 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8330 (tttt) cc_final: 0.8101 (mttt) REVERT: A 87 PHE cc_start: 0.8485 (p90) cc_final: 0.8102 (p90) REVERT: A 98 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7806 (mmmt) REVERT: A 120 ARG cc_start: 0.7874 (mtt180) cc_final: 0.7666 (mtt180) REVERT: A 169 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7112 (mm-30) REVERT: A 198 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7080 (t0) REVERT: A 236 ASP cc_start: 0.8500 (t0) cc_final: 0.8107 (t70) REVERT: A 240 LYS cc_start: 0.8757 (mmtm) cc_final: 0.8387 (mptt) REVERT: B 8 ARG cc_start: 0.7985 (ttt180) cc_final: 0.7664 (ttt180) REVERT: B 13 GLN cc_start: 0.8488 (tp40) cc_final: 0.7597 (tp40) REVERT: B 74 SER cc_start: 0.8357 (t) cc_final: 0.8020 (p) REVERT: B 119 ASN cc_start: 0.7825 (m-40) cc_final: 0.7488 (m110) REVERT: B 134 ARG cc_start: 0.8300 (ptp-110) cc_final: 0.8074 (ptp90) REVERT: B 204 CYS cc_start: 0.7881 (m) cc_final: 0.7593 (m) REVERT: N 14 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7639 (mm-40) REVERT: N 32 ASN cc_start: 0.8597 (m-40) cc_final: 0.8394 (m110) REVERT: N 61 TYR cc_start: 0.8518 (m-80) cc_final: 0.8014 (m-80) REVERT: R 26 PHE cc_start: 0.8051 (t80) cc_final: 0.7824 (t80) REVERT: R 36 PHE cc_start: 0.7830 (t80) cc_final: 0.7621 (t80) REVERT: R 149 MET cc_start: 0.6230 (tpt) cc_final: 0.5878 (tpt) REVERT: R 181 ILE cc_start: 0.8025 (mm) cc_final: 0.7792 (mm) REVERT: R 182 LEU cc_start: 0.8483 (tp) cc_final: 0.8272 (tt) REVERT: R 193 ILE cc_start: 0.8175 (tp) cc_final: 0.7975 (tp) REVERT: R 247 MET cc_start: 0.6563 (mmm) cc_final: 0.6218 (mmm) outliers start: 25 outliers final: 22 residues processed: 245 average time/residue: 0.1159 time to fit residues: 36.5838 Evaluate side-chains 253 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LYS 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 172 ARG Chi-restraints excluded: chain A residue 198 ASP 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 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: 3.9990 chunk 90 optimal weight: 0.0980 chunk 97 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3880 r_free = 0.3880 target = 0.139429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.121445 restraints weight = 12511.391| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.18 r_work: 0.3514 rms_B_bonded: 2.80 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: 0.7642 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8520 Z= 0.145 Angle : 0.511 6.595 11553 Z= 0.274 Chirality : 0.041 0.150 1312 Planarity : 0.004 0.042 1456 Dihedral : 4.093 19.431 1193 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 2.97 % Allowed : 16.81 % 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: 1.75 (0.26), residues: 1037 helix: 2.77 (0.23), residues: 442 sheet: 0.53 (0.33), 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 0.016 0.001 TYR B 59 PHE 0.016 0.001 PHE R 188 TRP 0.017 0.002 TRP R 88 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8518) covalent geometry : angle 0.51075 (11549) SS BOND : bond 0.00252 ( 2) SS BOND : angle 0.55223 ( 4) hydrogen bonds : bond 0.04167 ( 464) hydrogen bonds : angle 4.02247 ( 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 276 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 0.264 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: 0.7185 (mm110) REVERT: A 24 LYS cc_start: 0.8345 (tttt) cc_final: 0.8099 (mttt) REVERT: A 29 ASP cc_start: 0.7823 (t0) cc_final: 0.7338 (t0) REVERT: A 87 PHE cc_start: 0.8489 (p90) cc_final: 0.8039 (p90) REVERT: A 120 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7670 (mtt180) REVERT: A 169 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7048 (mm-30) REVERT: A 198 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7173 (t0) REVERT: A 236 ASP cc_start: 0.8539 (t0) cc_final: 0.8277 (t70) REVERT: B 8 ARG cc_start: 0.8049 (ttt180) cc_final: 0.7702 (ttt180) REVERT: B 13 GLN cc_start: 0.8485 (tp40) cc_final: 0.7579 (tp40) REVERT: B 74 SER cc_start: 0.8355 (t) cc_final: 0.8034 (p) REVERT: B 134 ARG cc_start: 0.8288 (ptp-110) cc_final: 0.8083 (ptp90) REVERT: B 204 CYS cc_start: 0.7999 (m) cc_final: 0.7741 (m) REVERT: B 246 ASP cc_start: 0.8229 (m-30) cc_final: 0.7937 (m-30) REVERT: N 14 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7695 (mm-40) REVERT: N 32 ASN cc_start: 0.8610 (m-40) cc_final: 0.8397 (m110) REVERT: N 61 TYR cc_start: 0.8523 (m-80) cc_final: 0.8004 (m-80) REVERT: N 109 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.6319 (m-80) REVERT: R 26 PHE cc_start: 0.8148 (t80) cc_final: 0.7933 (t80) REVERT: R 36 PHE cc_start: 0.7871 (t80) cc_final: 0.7650 (t80) REVERT: R 149 MET cc_start: 0.6273 (tpt) cc_final: 0.5921 (tpt) REVERT: R 193 ILE cc_start: 0.8283 (tp) cc_final: 0.8078 (tp) REVERT: R 222 LYS cc_start: 0.7832 (tmtt) cc_final: 0.7443 (tmtt) REVERT: R 247 MET cc_start: 0.6569 (mmm) cc_final: 0.6211 (mmm) outliers start: 27 outliers final: 22 residues processed: 255 average time/residue: 0.1153 time to fit residues: 37.9170 Evaluate side-chains 268 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 30 LYS 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 172 ARG Chi-restraints excluded: chain A residue 198 ASP 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 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: 0.7980 chunk 15 optimal weight: 0.0980 chunk 45 optimal weight: 0.0770 chunk 28 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 122 GLN B 119 ASN B 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.145970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.127490 restraints weight = 12521.213| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.25 r_work: 0.3527 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2335 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= 0.118 Angle : 0.504 6.677 11553 Z= 0.269 Chirality : 0.040 0.151 1312 Planarity : 0.004 0.042 1456 Dihedral : 4.014 18.932 1193 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.51 % Favored : 97.40 % Rotamer: Outliers : 2.53 % Allowed : 17.80 % Favored : 79.67 % 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: 2.80 (0.23), residues: 446 sheet: 0.48 (0.34), residues: 223 loop : -0.49 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.014 0.001 TYR R 241 PHE 0.017 0.001 PHE R 188 TRP 0.016 0.002 TRP R 300 HIS 0.003 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8518) covalent geometry : angle 0.50347 (11549) SS BOND : bond 0.00248 ( 2) SS BOND : angle 0.61493 ( 4) hydrogen bonds : bond 0.03902 ( 464) hydrogen bonds : angle 3.97268 ( 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 269 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8370 (tttt) cc_final: 0.8128 (mttt) REVERT: A 87 PHE cc_start: 0.8468 (p90) cc_final: 0.8042 (p90) REVERT: A 98 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7834 (mmmt) REVERT: A 120 ARG cc_start: 0.7882 (mtt180) cc_final: 0.7673 (mtt180) REVERT: A 122 GLN cc_start: 0.8291 (tp40) cc_final: 0.8028 (tp-100) REVERT: A 169 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7039 (mm-30) REVERT: A 198 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7133 (t0) REVERT: B 8 ARG cc_start: 0.8016 (ttt180) cc_final: 0.7672 (ttt180) REVERT: B 13 GLN cc_start: 0.8476 (tp40) cc_final: 0.7576 (tp40) REVERT: B 74 SER cc_start: 0.8329 (t) cc_final: 0.7995 (p) REVERT: B 119 ASN cc_start: 0.7506 (m-40) cc_final: 0.7045 (m110) REVERT: B 134 ARG cc_start: 0.8298 (ptp-110) cc_final: 0.8073 (ptp90) REVERT: B 204 CYS cc_start: 0.7935 (m) cc_final: 0.7673 (m) REVERT: B 246 ASP cc_start: 0.8232 (m-30) cc_final: 0.7945 (m-30) REVERT: B 277 SER cc_start: 0.8135 (p) cc_final: 0.7933 (m) REVERT: N 14 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7744 (mm-40) REVERT: N 32 ASN cc_start: 0.8570 (m-40) cc_final: 0.8354 (m110) REVERT: N 61 TYR cc_start: 0.8515 (m-80) cc_final: 0.8041 (m-80) REVERT: N 109 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.6293 (m-80) REVERT: R 26 PHE cc_start: 0.8014 (t80) cc_final: 0.7801 (t80) REVERT: R 36 PHE cc_start: 0.7863 (t80) cc_final: 0.7647 (t80) REVERT: R 149 MET cc_start: 0.6245 (tpt) cc_final: 0.5900 (tpt) REVERT: R 247 MET cc_start: 0.6542 (mmm) cc_final: 0.6185 (mmm) outliers start: 23 outliers final: 20 residues processed: 250 average time/residue: 0.1120 time to fit residues: 36.0208 Evaluate side-chains 265 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN 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 172 ARG Chi-restraints excluded: chain A residue 198 ASP 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 53 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 134 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 = 0.3901 r_free = 0.3901 target = 0.145025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126653 restraints weight = 12529.634| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.26 r_work: 0.3512 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8520 Z= 0.143 Angle : 0.526 6.790 11553 Z= 0.281 Chirality : 0.041 0.151 1312 Planarity : 0.004 0.042 1456 Dihedral : 4.044 19.498 1193 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 2.75 % Allowed : 18.79 % Favored : 78.46 % 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: 2.73 (0.23), residues: 443 sheet: 0.58 (0.35), residues: 203 loop : -0.56 (0.30), residues: 391 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 0.004 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8518) covalent geometry : angle 0.52598 (11549) SS BOND : bond 0.00262 ( 2) SS BOND : angle 0.56826 ( 4) hydrogen bonds : bond 0.04118 ( 464) hydrogen bonds : angle 3.99316 ( 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 276 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 251 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8355 (tttt) cc_final: 0.8111 (mttt) REVERT: A 29 ASP cc_start: 0.7832 (t0) cc_final: 0.7357 (t0) REVERT: A 87 PHE cc_start: 0.8464 (p90) cc_final: 0.8009 (p90) REVERT: A 98 LYS cc_start: 0.8175 (mmmt) cc_final: 0.7815 (mmmt) REVERT: A 120 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7673 (mtt180) REVERT: A 122 GLN cc_start: 0.8275 (tp40) cc_final: 0.8027 (tp-100) REVERT: A 134 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7437 (t0) REVERT: A 198 ASP cc_start: 0.7543 (t0) cc_final: 0.7173 (t0) REVERT: A 236 ASP cc_start: 0.8574 (t70) cc_final: 0.8071 (t0) REVERT: B 8 ARG cc_start: 0.8043 (ttt180) cc_final: 0.7690 (ttt180) REVERT: B 13 GLN cc_start: 0.8480 (tp40) cc_final: 0.7581 (tp40) REVERT: B 74 SER cc_start: 0.8368 (t) cc_final: 0.8050 (p) REVERT: B 119 ASN cc_start: 0.7750 (m-40) cc_final: 0.7318 (m110) REVERT: B 134 ARG cc_start: 0.8291 (ptp-110) cc_final: 0.8043 (ptp90) REVERT: B 204 CYS cc_start: 0.7984 (m) cc_final: 0.7745 (m) REVERT: B 246 ASP cc_start: 0.8248 (m-30) cc_final: 0.7955 (m-30) REVERT: B 277 SER cc_start: 0.8138 (p) cc_final: 0.7912 (m) REVERT: B 318 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7963 (tt) REVERT: N 14 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7753 (mm-40) REVERT: N 32 ASN cc_start: 0.8580 (m-40) cc_final: 0.8370 (m110) REVERT: N 61 TYR cc_start: 0.8525 (m-80) cc_final: 0.8015 (m-80) REVERT: N 109 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.6015 (m-80) REVERT: R 26 PHE cc_start: 0.8038 (t80) cc_final: 0.7829 (t80) REVERT: R 36 PHE cc_start: 0.7864 (t80) cc_final: 0.7632 (t80) REVERT: R 149 MET cc_start: 0.6263 (tpt) cc_final: 0.5902 (tpt) REVERT: R 222 LYS cc_start: 0.7856 (tmtt) cc_final: 0.7467 (tmtt) REVERT: R 247 MET cc_start: 0.6539 (mmm) cc_final: 0.6138 (mmm) outliers start: 25 outliers final: 22 residues processed: 256 average time/residue: 0.1161 time to fit residues: 38.3176 Evaluate side-chains 262 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 30 LYS 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 134 ASN Chi-restraints excluded: chain A residue 140 ILE 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 318 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: 6.9990 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 56 optimal weight: 0.2980 chunk 78 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 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 = 0.3887 r_free = 0.3887 target = 0.140088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.122015 restraints weight = 12508.808| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.19 r_work: 0.3523 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2406 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= 0.138 Angle : 0.533 7.405 11553 Z= 0.283 Chirality : 0.041 0.151 1312 Planarity : 0.004 0.042 1456 Dihedral : 4.035 19.500 1193 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.51 % Favored : 97.40 % Rotamer: Outliers : 2.75 % Allowed : 18.90 % Favored : 78.35 % 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: 1.67 (0.26), residues: 1037 helix: 2.70 (0.23), residues: 442 sheet: 0.52 (0.34), residues: 212 loop : -0.47 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.024 0.001 TYR R 106 PHE 0.018 0.001 PHE R 188 TRP 0.016 0.002 TRP R 300 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8518) covalent geometry : angle 0.53266 (11549) SS BOND : bond 0.00278 ( 2) SS BOND : angle 0.56324 ( 4) hydrogen bonds : bond 0.04095 ( 464) hydrogen bonds : angle 4.01081 ( 1335) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2331.60 seconds wall clock time: 40 minutes 30.54 seconds (2430.54 seconds total)