Starting phenix.real_space_refine on Sat Jul 26 07:11:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xp6_33366/07_2025/7xp6_33366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xp6_33366/07_2025/7xp6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xp6_33366/07_2025/7xp6_33366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xp6_33366/07_2025/7xp6_33366.map" model { file = "/net/cci-nas-00/data/ceres_data/7xp6_33366/07_2025/7xp6_33366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xp6_33366/07_2025/7xp6_33366.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.18, per 1000 atoms: 0.86 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: 2.96 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.56 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: 4.86 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 161.140 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: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 33.320 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 198.330 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.014 0.001 TRP A 99 HIS 0.005 0.001 HIS A 212 PHE 0.026 0.001 PHE R 9 TYR 0.029 0.002 TYR B 59 ARG 0.009 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.17062 ( 464) hydrogen bonds : angle 6.36902 ( 1335) SS BOND : bond 0.00307 ( 2) SS BOND : angle 0.69877 ( 4) covalent geometry : bond 0.00320 ( 8518) covalent geometry : angle 0.59273 (11549) *********************** 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 : 0.856 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: 0.3436 time to fit residues: 102.2206 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 : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.146721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.128498 restraints weight = 12337.363| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.21 r_work: 0.3527 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1202 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= 0.154 Angle : 0.542 7.453 11553 Z= 0.296 Chirality : 0.043 0.192 1312 Planarity : 0.005 0.072 1456 Dihedral : 8.290 151.875 1193 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.65 % Allowed : 8.02 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.26), residues: 1037 helix: 2.82 (0.23), residues: 439 sheet: 0.90 (0.33), residues: 247 loop : -0.45 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.005 0.001 HIS A 212 PHE 0.025 0.002 PHE A 87 TYR 0.025 0.002 TYR B 59 ARG 0.006 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.04945 ( 464) hydrogen bonds : angle 4.57041 ( 1335) SS BOND : bond 0.00157 ( 2) SS BOND : angle 1.01526 ( 4) covalent geometry : bond 0.00330 ( 8518) covalent geometry : angle 0.54143 (11549) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 249 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8360 (tttt) cc_final: 0.8121 (mttt) REVERT: A 87 PHE cc_start: 0.8206 (p90) cc_final: 0.7929 (p90) REVERT: A 129 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8422 (ttpp) REVERT: A 188 ARG cc_start: 0.8385 (mtm180) cc_final: 0.8044 (mtm-85) REVERT: A 226 ASN cc_start: 0.8478 (m110) cc_final: 0.8107 (m-40) REVERT: A 232 ASP cc_start: 0.7865 (m-30) cc_final: 0.7663 (m-30) REVERT: B 8 ARG cc_start: 0.8099 (ttt180) cc_final: 0.7769 (ttt180) REVERT: B 13 GLN cc_start: 0.8489 (tp40) cc_final: 0.7585 (tp40) REVERT: B 45 MET cc_start: 0.8813 (mtp) cc_final: 0.8535 (mtp) REVERT: B 119 ASN cc_start: 0.7813 (m-40) cc_final: 0.7595 (m110) REVERT: B 134 ARG cc_start: 0.8268 (ptp-110) cc_final: 0.8026 (ptp90) REVERT: B 264 TYR cc_start: 0.8620 (m-80) cc_final: 0.8168 (m-80) REVERT: G 19 LEU cc_start: 0.8543 (mm) cc_final: 0.8335 (mm) REVERT: N 14 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7615 (mm110) REVERT: N 32 ASN cc_start: 0.8744 (m-40) cc_final: 0.8525 (m110) REVERT: N 53 SER cc_start: 0.8621 (t) cc_final: 0.8303 (p) REVERT: N 61 TYR cc_start: 0.8519 (m-80) cc_final: 0.8060 (m-80) REVERT: N 121 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7874 (mm-40) REVERT: R 36 PHE cc_start: 0.7854 (t80) cc_final: 0.7605 (t80) REVERT: R 149 MET cc_start: 0.6323 (tpt) cc_final: 0.5976 (tpt) REVERT: R 181 ILE cc_start: 0.7912 (mm) cc_final: 0.7663 (mm) REVERT: R 182 LEU cc_start: 0.8517 (tp) cc_final: 0.8282 (tt) REVERT: R 193 ILE cc_start: 0.8305 (tp) cc_final: 0.8098 (tp) REVERT: R 222 LYS cc_start: 0.7782 (tmtt) cc_final: 0.7481 (tmtt) REVERT: R 280 ILE cc_start: 0.8718 (mt) cc_final: 0.8506 (mm) REVERT: R 285 LYS cc_start: 0.8699 (pptt) cc_final: 0.8470 (pptt) outliers start: 15 outliers final: 13 residues processed: 249 average time/residue: 0.2667 time to fit residues: 84.8348 Evaluate side-chains 255 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 242 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 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 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 = 0.3882 r_free = 0.3882 target = 0.139561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121805 restraints weight = 12692.253| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.18 r_work: 0.3523 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8520 Z= 0.150 Angle : 0.524 8.590 11553 Z= 0.282 Chirality : 0.042 0.183 1312 Planarity : 0.004 0.059 1456 Dihedral : 7.811 142.423 1193 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.31 % Allowed : 10.66 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.26), residues: 1037 helix: 2.84 (0.23), residues: 440 sheet: 0.78 (0.33), residues: 234 loop : -0.44 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 66 HIS 0.004 0.001 HIS A 212 PHE 0.016 0.001 PHE R 188 TYR 0.021 0.001 TYR B 59 ARG 0.004 0.000 ARG A 120 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 464) hydrogen bonds : angle 4.32455 ( 1335) SS BOND : bond 0.00228 ( 2) SS BOND : angle 0.87971 ( 4) covalent geometry : bond 0.00327 ( 8518) covalent geometry : angle 0.52378 (11549) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8334 (tttt) cc_final: 0.8111 (mttt) REVERT: A 87 PHE cc_start: 0.8314 (p90) cc_final: 0.8015 (p90) REVERT: A 129 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8397 (ttpp) REVERT: A 226 ASN cc_start: 0.8433 (m110) cc_final: 0.8072 (m-40) REVERT: A 232 ASP cc_start: 0.7880 (m-30) cc_final: 0.7665 (m-30) REVERT: B 8 ARG cc_start: 0.7990 (ttt180) cc_final: 0.7732 (ttt180) REVERT: B 13 GLN cc_start: 0.8484 (tp40) cc_final: 0.7584 (tp40) REVERT: B 119 ASN cc_start: 0.7994 (m-40) cc_final: 0.7636 (m110) REVERT: B 134 ARG cc_start: 0.8239 (ptp-110) cc_final: 0.8021 (ptp90) REVERT: N 14 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7628 (mm110) REVERT: N 32 ASN cc_start: 0.8720 (m-40) cc_final: 0.8490 (m110) REVERT: N 53 SER cc_start: 0.8621 (t) cc_final: 0.8292 (p) REVERT: N 61 TYR cc_start: 0.8507 (m-80) cc_final: 0.8075 (m-80) REVERT: R 36 PHE cc_start: 0.7838 (t80) cc_final: 0.7608 (t80) REVERT: R 149 MET cc_start: 0.6291 (tpt) cc_final: 0.5925 (tpt) REVERT: R 181 ILE cc_start: 0.7978 (mm) cc_final: 0.7711 (mm) REVERT: R 182 LEU cc_start: 0.8501 (tp) cc_final: 0.8271 (tt) REVERT: R 193 ILE cc_start: 0.8273 (tp) cc_final: 0.8052 (tp) REVERT: R 222 LYS cc_start: 0.7798 (tmtt) cc_final: 0.7483 (tmtt) outliers start: 21 outliers final: 16 residues processed: 248 average time/residue: 0.3274 time to fit residues: 106.5734 Evaluate side-chains 260 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 74 optimal weight: 0.0370 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 98 optimal weight: 0.9980 chunk 94 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.140077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.122174 restraints weight = 12494.610| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.18 r_work: 0.3535 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8520 Z= 0.125 Angle : 0.499 7.163 11553 Z= 0.267 Chirality : 0.040 0.165 1312 Planarity : 0.004 0.053 1456 Dihedral : 5.452 102.030 1193 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.86 % Allowed : 12.09 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.26), residues: 1037 helix: 2.92 (0.23), residues: 440 sheet: 0.65 (0.33), residues: 236 loop : -0.45 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 212 PHE 0.017 0.001 PHE R 188 TYR 0.016 0.001 TYR B 59 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 464) hydrogen bonds : angle 4.14225 ( 1335) SS BOND : bond 0.00234 ( 2) SS BOND : angle 0.75972 ( 4) covalent geometry : bond 0.00266 ( 8518) covalent geometry : angle 0.49862 (11549) *********************** 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 274 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8315 (tttt) cc_final: 0.8090 (mttt) REVERT: A 29 ASP cc_start: 0.7790 (t0) cc_final: 0.7309 (t0) REVERT: A 87 PHE cc_start: 0.8351 (p90) cc_final: 0.8000 (p90) REVERT: A 106 VAL cc_start: 0.8177 (t) cc_final: 0.7830 (m) REVERT: A 169 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7280 (mm-30) REVERT: A 226 ASN cc_start: 0.8399 (m110) cc_final: 0.8054 (m-40) REVERT: A 232 ASP cc_start: 0.7870 (m-30) cc_final: 0.7639 (m-30) REVERT: B 8 ARG cc_start: 0.8011 (ttt180) cc_final: 0.7719 (ttt180) REVERT: B 13 GLN cc_start: 0.8453 (tp40) cc_final: 0.7545 (tp40) REVERT: B 75 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8463 (mm-40) REVERT: B 119 ASN cc_start: 0.7926 (m-40) cc_final: 0.7639 (m110) REVERT: B 134 ARG cc_start: 0.8290 (ptp-110) cc_final: 0.8042 (ptp90) REVERT: B 212 ASP cc_start: 0.8151 (t0) cc_final: 0.7842 (t0) REVERT: B 262 MET cc_start: 0.7970 (tpt) cc_final: 0.7749 (tpt) REVERT: N 14 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7612 (mm-40) REVERT: N 32 ASN cc_start: 0.8673 (m-40) cc_final: 0.8459 (m110) REVERT: N 53 SER cc_start: 0.8628 (t) cc_final: 0.8273 (p) REVERT: N 61 TYR cc_start: 0.8519 (m-80) cc_final: 0.8022 (m-80) REVERT: R 26 PHE cc_start: 0.8192 (t80) cc_final: 0.7872 (t80) REVERT: R 36 PHE cc_start: 0.7855 (t80) cc_final: 0.7631 (t80) REVERT: R 149 MET cc_start: 0.6311 (tpt) cc_final: 0.5932 (tpt) REVERT: R 181 ILE cc_start: 0.7990 (mm) cc_final: 0.7730 (mm) REVERT: R 182 LEU cc_start: 0.8521 (tp) cc_final: 0.8305 (tt) REVERT: R 193 ILE cc_start: 0.8301 (tp) cc_final: 0.8075 (tp) REVERT: R 247 MET cc_start: 0.6590 (mmm) cc_final: 0.6350 (mmm) outliers start: 26 outliers final: 16 residues processed: 256 average time/residue: 0.3454 time to fit residues: 114.8699 Evaluate side-chains 258 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 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 104 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 33 optimal weight: 0.0970 chunk 11 optimal weight: 0.0870 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN 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 = 0.3894 r_free = 0.3894 target = 0.140438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.122538 restraints weight = 12498.080| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.19 r_work: 0.3538 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8520 Z= 0.116 Angle : 0.493 6.319 11553 Z= 0.264 Chirality : 0.040 0.206 1312 Planarity : 0.004 0.049 1456 Dihedral : 4.113 18.468 1193 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.08 % Allowed : 14.18 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.26), residues: 1037 helix: 2.89 (0.23), residues: 440 sheet: 0.60 (0.33), residues: 235 loop : -0.45 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 66 HIS 0.003 0.001 HIS A 212 PHE 0.018 0.001 PHE R 188 TYR 0.013 0.001 TYR B 59 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 464) hydrogen bonds : angle 4.06619 ( 1335) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.69053 ( 4) covalent geometry : bond 0.00248 ( 8518) covalent geometry : angle 0.49270 (11549) *********************** 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 265 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8300 (tttt) cc_final: 0.8076 (mttt) REVERT: A 29 ASP cc_start: 0.7794 (t0) cc_final: 0.7284 (t0) REVERT: A 87 PHE cc_start: 0.8399 (p90) cc_final: 0.8025 (p90) REVERT: A 92 GLN cc_start: 0.8508 (mp10) cc_final: 0.8205 (mp10) REVERT: A 169 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7186 (mm-30) REVERT: A 198 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.7086 (t0) REVERT: A 232 ASP cc_start: 0.7844 (m-30) cc_final: 0.7626 (m-30) REVERT: B 8 ARG cc_start: 0.7951 (ttt180) cc_final: 0.7647 (ttt180) REVERT: B 13 GLN cc_start: 0.8494 (tp40) cc_final: 0.7594 (tp40) REVERT: B 134 ARG cc_start: 0.8282 (ptp-110) cc_final: 0.8039 (ptp90) REVERT: B 262 MET cc_start: 0.8078 (tpt) cc_final: 0.7839 (tpt) REVERT: N 14 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7659 (mm-40) REVERT: N 32 ASN cc_start: 0.8643 (m-40) cc_final: 0.8430 (m110) REVERT: R 26 PHE cc_start: 0.8145 (t80) cc_final: 0.7862 (t80) REVERT: R 36 PHE cc_start: 0.7829 (t80) cc_final: 0.7611 (t80) REVERT: R 149 MET cc_start: 0.6334 (tpt) cc_final: 0.5962 (tpt) REVERT: R 181 ILE cc_start: 0.7988 (mm) cc_final: 0.7731 (mm) REVERT: R 182 LEU cc_start: 0.8474 (tp) cc_final: 0.8248 (tt) REVERT: R 193 ILE cc_start: 0.8285 (tp) cc_final: 0.8069 (tp) REVERT: R 247 MET cc_start: 0.6562 (mmm) cc_final: 0.6272 (mmm) outliers start: 28 outliers final: 20 residues processed: 243 average time/residue: 0.3333 time to fit residues: 104.7396 Evaluate side-chains 254 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 233 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 198 ASP 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 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 8 optimal weight: 0.0570 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 119 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 = 0.3880 r_free = 0.3880 target = 0.139176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.121115 restraints weight = 12523.236| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.19 r_work: 0.3518 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8520 Z= 0.161 Angle : 0.514 5.612 11553 Z= 0.278 Chirality : 0.041 0.149 1312 Planarity : 0.004 0.046 1456 Dihedral : 4.136 19.167 1193 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 3.08 % Allowed : 15.16 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.26), residues: 1037 helix: 2.80 (0.23), residues: 440 sheet: 0.60 (0.33), residues: 232 loop : -0.52 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 66 HIS 0.004 0.001 HIS A 85 PHE 0.016 0.001 PHE R 188 TYR 0.016 0.001 TYR B 59 ARG 0.002 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 464) hydrogen bonds : angle 4.09654 ( 1335) SS BOND : bond 0.00260 ( 2) SS BOND : angle 0.59114 ( 4) covalent geometry : bond 0.00355 ( 8518) covalent geometry : angle 0.51380 (11549) *********************** 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: 28 poor density : 260 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8307 (tttt) cc_final: 0.8098 (mttt) REVERT: A 29 ASP cc_start: 0.7823 (t0) cc_final: 0.7342 (t0) REVERT: A 87 PHE cc_start: 0.8453 (p90) cc_final: 0.8046 (p90) REVERT: A 122 GLN cc_start: 0.8399 (tp-100) cc_final: 0.8156 (tp-100) REVERT: A 169 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7138 (mm-30) REVERT: A 198 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7151 (t0) REVERT: A 226 ASN cc_start: 0.8461 (m110) cc_final: 0.8113 (m-40) REVERT: A 232 ASP cc_start: 0.7936 (m-30) cc_final: 0.7725 (m-30) REVERT: B 8 ARG cc_start: 0.7984 (ttt180) cc_final: 0.7677 (ttt180) REVERT: B 13 GLN cc_start: 0.8492 (tp40) cc_final: 0.7590 (tp40) REVERT: B 74 SER cc_start: 0.8374 (t) cc_final: 0.8134 (m) REVERT: B 119 ASN cc_start: 0.7880 (m-40) cc_final: 0.7510 (m110) REVERT: B 134 ARG cc_start: 0.8301 (ptp-110) cc_final: 0.8063 (ptp90) REVERT: B 262 MET cc_start: 0.8102 (tpt) cc_final: 0.7854 (tpt) REVERT: N 14 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7630 (mm-40) REVERT: N 32 ASN cc_start: 0.8658 (m-40) cc_final: 0.8426 (m110) REVERT: N 61 TYR cc_start: 0.8527 (m-80) cc_final: 0.8035 (m-80) REVERT: R 26 PHE cc_start: 0.8184 (t80) cc_final: 0.7898 (t80) REVERT: R 36 PHE cc_start: 0.7811 (t80) cc_final: 0.7596 (t80) REVERT: R 149 MET cc_start: 0.6331 (tpt) cc_final: 0.5944 (tpt) REVERT: R 181 ILE cc_start: 0.8042 (mm) cc_final: 0.7831 (mm) REVERT: R 182 LEU cc_start: 0.8534 (tp) cc_final: 0.8322 (tt) REVERT: R 193 ILE cc_start: 0.8304 (tp) cc_final: 0.8103 (tp) REVERT: R 222 LYS cc_start: 0.7791 (tmtt) cc_final: 0.7433 (tmtt) REVERT: R 247 MET cc_start: 0.6577 (mmm) cc_final: 0.6241 (mmm) outliers start: 28 outliers final: 23 residues processed: 266 average time/residue: 0.3019 time to fit residues: 103.2264 Evaluate side-chains 274 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 250 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 241 GLU 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 27 ILE 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 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 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.0010 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 155 ASN R 224 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.137965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.119910 restraints weight = 12554.903| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.19 r_work: 0.3500 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8520 Z= 0.194 Angle : 0.538 6.707 11553 Z= 0.292 Chirality : 0.042 0.145 1312 Planarity : 0.004 0.044 1456 Dihedral : 4.309 21.709 1193 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.99 % Favored : 96.82 % Rotamer: Outliers : 3.08 % Allowed : 16.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.26), residues: 1037 helix: 2.66 (0.23), residues: 441 sheet: 0.54 (0.32), residues: 230 loop : -0.50 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 99 HIS 0.004 0.001 HIS R 205 PHE 0.017 0.001 PHE R 188 TYR 0.019 0.002 TYR B 59 ARG 0.003 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 464) hydrogen bonds : angle 4.20347 ( 1335) SS BOND : bond 0.00256 ( 2) SS BOND : angle 0.57990 ( 4) covalent geometry : bond 0.00428 ( 8518) covalent geometry : angle 0.53791 (11549) *********************** 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 284 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8340 (tttt) cc_final: 0.8112 (mttt) REVERT: A 29 ASP cc_start: 0.7847 (t0) cc_final: 0.7406 (t0) REVERT: A 87 PHE cc_start: 0.8460 (p90) cc_final: 0.8054 (p90) REVERT: A 122 GLN cc_start: 0.8389 (tp-100) cc_final: 0.8090 (tp-100) REVERT: A 169 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7131 (mm-30) REVERT: A 198 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7222 (t0) REVERT: A 226 ASN cc_start: 0.8540 (m110) cc_final: 0.8158 (m-40) REVERT: A 232 ASP cc_start: 0.7983 (m-30) cc_final: 0.7782 (m-30) REVERT: B 8 ARG cc_start: 0.7934 (ttt180) cc_final: 0.7620 (ttt180) REVERT: B 13 GLN cc_start: 0.8499 (tp40) cc_final: 0.7622 (tp40) REVERT: B 74 SER cc_start: 0.8352 (t) cc_final: 0.8108 (m) REVERT: B 134 ARG cc_start: 0.8290 (ptp-110) cc_final: 0.8076 (ptp90) REVERT: B 204 CYS cc_start: 0.7948 (m) cc_final: 0.7712 (m) REVERT: N 14 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7624 (mm-40) REVERT: N 32 ASN cc_start: 0.8673 (m-40) cc_final: 0.8444 (m110) REVERT: N 61 TYR cc_start: 0.8568 (m-80) cc_final: 0.8099 (m-80) REVERT: N 109 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.6541 (m-80) REVERT: R 26 PHE cc_start: 0.8293 (t80) cc_final: 0.7964 (t80) REVERT: R 36 PHE cc_start: 0.7857 (t80) cc_final: 0.7642 (t80) REVERT: R 149 MET cc_start: 0.6294 (tpt) cc_final: 0.5922 (tpt) REVERT: R 182 LEU cc_start: 0.8578 (tp) cc_final: 0.8337 (tt) REVERT: R 222 LYS cc_start: 0.7879 (tmtt) cc_final: 0.7490 (tmtt) REVERT: R 247 MET cc_start: 0.6588 (mmm) cc_final: 0.6253 (mmm) outliers start: 28 outliers final: 24 residues processed: 264 average time/residue: 0.3773 time to fit residues: 131.6634 Evaluate side-chains 273 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR 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 27 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 81 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 67 optimal weight: 0.4980 chunk 8 optimal weight: 0.0060 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 79 optimal weight: 0.5980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.140189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.122085 restraints weight = 12597.129| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.20 r_work: 0.3531 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8520 Z= 0.116 Angle : 0.508 7.960 11553 Z= 0.271 Chirality : 0.040 0.149 1312 Planarity : 0.004 0.044 1456 Dihedral : 4.079 19.800 1193 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.51 % Favored : 97.30 % Rotamer: Outliers : 2.97 % Allowed : 16.92 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.26), residues: 1037 helix: 2.77 (0.23), residues: 443 sheet: 0.52 (0.33), residues: 230 loop : -0.42 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 300 HIS 0.003 0.001 HIS A 212 PHE 0.017 0.001 PHE R 188 TYR 0.014 0.001 TYR R 241 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 464) hydrogen bonds : angle 4.00301 ( 1335) SS BOND : bond 0.00243 ( 2) SS BOND : angle 0.63923 ( 4) covalent geometry : bond 0.00250 ( 8518) covalent geometry : angle 0.50780 (11549) *********************** 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 274 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8314 (tttt) cc_final: 0.8089 (mttt) REVERT: A 87 PHE cc_start: 0.8452 (p90) cc_final: 0.7999 (p90) REVERT: A 92 GLN cc_start: 0.8532 (mp10) cc_final: 0.8225 (mp10) REVERT: A 98 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7814 (mmmt) REVERT: A 122 GLN cc_start: 0.8404 (tp-100) cc_final: 0.8187 (tp40) REVERT: A 169 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7061 (mm-30) REVERT: A 198 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7124 (t0) REVERT: A 236 ASP cc_start: 0.8514 (t0) cc_final: 0.8158 (t70) REVERT: A 240 LYS cc_start: 0.8761 (mmtm) cc_final: 0.8440 (mptt) REVERT: B 8 ARG cc_start: 0.7990 (ttt180) cc_final: 0.7652 (ttt180) REVERT: B 13 GLN cc_start: 0.8488 (tp40) cc_final: 0.7597 (tp40) REVERT: B 74 SER cc_start: 0.8361 (t) cc_final: 0.8045 (p) REVERT: B 119 ASN cc_start: 0.7450 (m-40) cc_final: 0.6981 (m110) REVERT: B 134 ARG cc_start: 0.8320 (ptp-110) cc_final: 0.8117 (ptp90) REVERT: B 204 CYS cc_start: 0.7839 (m) cc_final: 0.7552 (m) REVERT: N 14 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7658 (mm-40) REVERT: N 32 ASN cc_start: 0.8599 (m-40) cc_final: 0.8384 (m110) REVERT: N 61 TYR cc_start: 0.8531 (m-80) cc_final: 0.8043 (m-80) REVERT: R 26 PHE cc_start: 0.8123 (t80) cc_final: 0.7749 (t80) REVERT: R 36 PHE cc_start: 0.7789 (t80) cc_final: 0.7583 (t80) REVERT: R 106 TYR cc_start: 0.8421 (m-10) cc_final: 0.8187 (m-10) REVERT: R 149 MET cc_start: 0.6225 (tpt) cc_final: 0.5872 (tpt) REVERT: R 222 LYS cc_start: 0.7758 (tmtt) cc_final: 0.7344 (tmtt) REVERT: R 247 MET cc_start: 0.6572 (mmm) cc_final: 0.6224 (mmm) outliers start: 27 outliers final: 23 residues processed: 252 average time/residue: 0.2634 time to fit residues: 84.9425 Evaluate side-chains 258 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 241 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 36 ASN Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 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 64 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 0.0570 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.139331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.120833 restraints weight = 12604.834| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.31 r_work: 0.3507 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2296 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= 0.149 Angle : 0.531 7.314 11553 Z= 0.284 Chirality : 0.041 0.150 1312 Planarity : 0.004 0.043 1456 Dihedral : 4.130 20.030 1193 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.89 % Favored : 96.91 % Rotamer: Outliers : 2.86 % Allowed : 17.58 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.26), residues: 1037 helix: 2.69 (0.23), residues: 443 sheet: 0.47 (0.32), residues: 230 loop : -0.44 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 300 HIS 0.003 0.001 HIS A 85 PHE 0.016 0.001 PHE R 188 TYR 0.016 0.001 TYR B 59 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 464) hydrogen bonds : angle 4.05400 ( 1335) SS BOND : bond 0.00252 ( 2) SS BOND : angle 0.55728 ( 4) covalent geometry : bond 0.00328 ( 8518) covalent geometry : angle 0.53060 (11549) *********************** 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 268 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8088 (tttt) cc_final: 0.7861 (mttt) REVERT: A 29 ASP cc_start: 0.7535 (t0) cc_final: 0.7037 (t0) REVERT: A 87 PHE cc_start: 0.8413 (p90) cc_final: 0.7944 (p90) REVERT: A 122 GLN cc_start: 0.8264 (tp-100) cc_final: 0.8004 (tp40) REVERT: A 198 ASP cc_start: 0.7360 (t0) cc_final: 0.6953 (t0) REVERT: A 236 ASP cc_start: 0.8305 (t0) cc_final: 0.8035 (t70) REVERT: A 248 LEU cc_start: 0.8340 (mt) cc_final: 0.8122 (mp) REVERT: B 8 ARG cc_start: 0.7850 (ttt180) cc_final: 0.7511 (ttt180) REVERT: B 13 GLN cc_start: 0.8336 (tp40) cc_final: 0.7408 (tp40) REVERT: B 74 SER cc_start: 0.8253 (t) cc_final: 0.7947 (p) REVERT: B 119 ASN cc_start: 0.7728 (m-40) cc_final: 0.7380 (m110) REVERT: B 134 ARG cc_start: 0.8105 (ptp-110) cc_final: 0.7897 (ptp90) REVERT: B 204 CYS cc_start: 0.7689 (m) cc_final: 0.7454 (m) REVERT: B 325 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7902 (mtp) REVERT: N 14 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7459 (mm-40) REVERT: N 32 ASN cc_start: 0.8522 (m-40) cc_final: 0.8297 (m110) REVERT: N 61 TYR cc_start: 0.8452 (m-80) cc_final: 0.7987 (m-80) REVERT: R 26 PHE cc_start: 0.8093 (t80) cc_final: 0.7850 (t80) REVERT: R 149 MET cc_start: 0.6058 (tpt) cc_final: 0.5702 (tpt) REVERT: R 222 LYS cc_start: 0.7682 (tmtt) cc_final: 0.7271 (tmtt) REVERT: R 247 MET cc_start: 0.6399 (mmm) cc_final: 0.6038 (mmm) outliers start: 26 outliers final: 24 residues processed: 247 average time/residue: 0.2568 time to fit residues: 81.1811 Evaluate side-chains 265 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 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 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 36 ASN Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 87 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 102 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 0.0050 overall best weight: 0.3552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN R 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.140904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.122703 restraints weight = 12523.813| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.21 r_work: 0.3531 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.002 0.031 8520 Z= 0.114 Angle : 0.524 8.112 11553 Z= 0.276 Chirality : 0.040 0.150 1312 Planarity : 0.004 0.043 1456 Dihedral : 4.012 19.240 1193 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.60 % Favored : 97.20 % Rotamer: Outliers : 3.08 % Allowed : 17.36 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.26), residues: 1037 helix: 2.73 (0.23), residues: 448 sheet: 0.46 (0.33), residues: 221 loop : -0.51 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 97 HIS 0.003 0.001 HIS A 212 PHE 0.018 0.001 PHE R 36 TYR 0.014 0.001 TYR R 241 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 464) hydrogen bonds : angle 3.94050 ( 1335) SS BOND : bond 0.00229 ( 2) SS BOND : angle 0.65270 ( 4) covalent geometry : bond 0.00247 ( 8518) covalent geometry : angle 0.52375 (11549) ********************** 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 267 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8344 (tttt) cc_final: 0.8116 (mttt) REVERT: A 87 PHE cc_start: 0.8455 (p90) cc_final: 0.7998 (p90) REVERT: A 98 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7892 (mmmt) REVERT: A 120 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7512 (mtm-85) REVERT: A 198 ASP cc_start: 0.7534 (t0) cc_final: 0.7148 (t0) REVERT: B 8 ARG cc_start: 0.8026 (ttt180) cc_final: 0.7681 (ttt180) REVERT: B 13 GLN cc_start: 0.8448 (tp40) cc_final: 0.7551 (tp40) REVERT: B 74 SER cc_start: 0.8393 (t) cc_final: 0.8070 (p) REVERT: B 119 ASN cc_start: 0.7516 (m-40) cc_final: 0.7125 (m110) REVERT: B 204 CYS cc_start: 0.7862 (m) cc_final: 0.7573 (m) REVERT: B 246 ASP cc_start: 0.8225 (m-30) cc_final: 0.7932 (m-30) REVERT: B 325 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8185 (mtp) REVERT: N 14 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7746 (mm-40) REVERT: N 32 ASN cc_start: 0.8545 (m-40) cc_final: 0.8343 (m110) REVERT: N 61 TYR cc_start: 0.8505 (m-80) cc_final: 0.8045 (m-80) REVERT: R 149 MET cc_start: 0.6208 (tpt) cc_final: 0.5844 (tpt) REVERT: R 247 MET cc_start: 0.6513 (mmm) cc_final: 0.6160 (mmm) outliers start: 28 outliers final: 21 residues processed: 243 average time/residue: 0.2562 time to fit residues: 79.5962 Evaluate side-chains 247 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 241 GLU 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 B residue 325 MET Chi-restraints excluded: chain N residue 36 ASN Chi-restraints excluded: chain N residue 53 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 78 optimal weight: 0.2980 chunk 19 optimal weight: 0.3980 chunk 76 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 224 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.139798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.121400 restraints weight = 12563.786| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.24 r_work: 0.3516 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2424 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 : 0.547 8.683 11553 Z= 0.287 Chirality : 0.041 0.151 1312 Planarity : 0.004 0.043 1456 Dihedral : 4.053 19.573 1193 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.89 % Favored : 96.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.26), residues: 1037 helix: 2.60 (0.24), residues: 449 sheet: 0.47 (0.34), residues: 214 loop : -0.47 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 97 HIS 0.003 0.001 HIS A 85 PHE 0.016 0.001 PHE R 188 TYR 0.015 0.001 TYR B 59 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 464) hydrogen bonds : angle 3.99313 ( 1335) SS BOND : bond 0.00255 ( 2) SS BOND : angle 0.55897 ( 4) covalent geometry : bond 0.00315 ( 8518) covalent geometry : angle 0.54737 (11549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5892.71 seconds wall clock time: 107 minutes 57.01 seconds (6477.01 seconds total)