Starting phenix.real_space_refine on Tue Sep 24 16:21:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/09_2024/7xp6_33366.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/09_2024/7xp6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/09_2024/7xp6_33366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/09_2024/7xp6_33366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/09_2024/7xp6_33366.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/09_2024/7xp6_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.37, per 1000 atoms: 0.64 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: 2.38 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: 0.88 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: 2.43 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2696 1.34 - 1.46: 1999 1.46 - 1.58: 3757 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 8518 Sorted by residual: bond pdb=" CAV SY9 R 501 " pdb=" NAY SY9 R 501 " ideal model delta sigma weight residual 1.454 1.501 -0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" CAG SY9 R 501 " pdb=" CAV SY9 R 501 " ideal model delta sigma weight residual 1.578 1.544 0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" CAX SY9 R 501 " pdb=" NAY SY9 R 501 " ideal model delta sigma weight residual 1.449 1.482 -0.033 2.00e-02 2.50e+03 2.78e+00 bond pdb=" N THR N 112 " pdb=" CA THR N 112 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.50e+00 bond pdb=" CAM SY9 R 501 " pdb=" OAO SY9 R 501 " ideal model delta sigma weight residual 1.411 1.434 -0.023 2.00e-02 2.50e+03 1.35e+00 ... (remaining 8513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11366 2.00 - 4.01: 163 4.01 - 6.01: 18 6.01 - 8.02: 1 8.02 - 10.02: 1 Bond angle restraints: 11549 Sorted by residual: angle pdb=" CA PRO R 187 " pdb=" N PRO R 187 " pdb=" CD PRO R 187 " ideal model delta sigma weight residual 112.00 106.05 5.95 1.40e+00 5.10e-01 1.80e+01 angle pdb=" C GLY A 159 " pdb=" N LYS A 160 " pdb=" CA LYS A 160 " ideal model delta sigma weight residual 121.54 127.94 -6.40 1.91e+00 2.74e-01 1.12e+01 angle pdb=" CB MET R 247 " pdb=" CG MET R 247 " pdb=" SD MET R 247 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CA ARG A 172 " pdb=" CB ARG A 172 " pdb=" CG ARG A 172 " ideal model delta sigma weight residual 114.10 119.64 -5.54 2.00e+00 2.50e-01 7.66e+00 angle pdb=" C ASP B 247 " pdb=" N ALA B 248 " pdb=" CA ALA B 248 " ideal model delta sigma weight residual 122.74 126.63 -3.89 1.44e+00 4.82e-01 7.29e+00 ... (remaining 11544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 5019 34.38 - 68.76: 74 68.76 - 103.14: 2 103.14 - 137.51: 3 137.51 - 171.89: 1 Dihedral angle restraints: 5099 sinusoidal: 2045 harmonic: 3054 Sorted by residual: dihedral pdb=" CAM SY9 R 501 " pdb=" CAP SY9 R 501 " pdb=" OAO SY9 R 501 " pdb=" CAQ SY9 R 501 " ideal model delta sinusoidal sigma weight residual -84.84 87.05 -171.89 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CAR SY9 R 501 " pdb=" CAP SY9 R 501 " pdb=" CAQ SY9 R 501 " pdb=" OAO SY9 R 501 " ideal model delta sinusoidal sigma weight residual 65.89 -56.55 122.44 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 5096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1073 0.051 - 0.101: 192 0.101 - 0.152: 42 0.152 - 0.203: 3 0.203 - 0.253: 2 Chirality restraints: 1312 Sorted by residual: chirality pdb=" NAY SY9 R 501 " pdb=" CAS SY9 R 501 " pdb=" CAV SY9 R 501 " pdb=" CAX SY9 R 501 " both_signs ideal model delta sigma weight residual False -2.12 -2.38 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CAK SY9 R 501 " pdb=" CAG SY9 R 501 " pdb=" CAN SY9 R 501 " pdb=" NAH SY9 R 501 " both_signs ideal model delta sigma weight residual False 2.54 2.77 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 1309 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAA SY9 R 501 " 0.233 2.00e-02 2.50e+03 1.59e-01 3.81e+02 pdb=" CAI SY9 R 501 " -0.048 2.00e-02 2.50e+03 pdb=" CAK SY9 R 501 " -0.105 2.00e-02 2.50e+03 pdb=" CAL SY9 R 501 " 0.202 2.00e-02 2.50e+03 pdb=" NAH SY9 R 501 " -0.189 2.00e-02 2.50e+03 pdb=" OAJ SY9 R 501 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 186 " -0.085 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO R 187 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO R 187 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO R 187 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 271 " -0.047 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO R 272 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO R 272 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 272 " -0.040 5.00e-02 4.00e+02 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 120 2.66 - 3.22: 7959 3.22 - 3.78: 12954 3.78 - 4.34: 17208 4.34 - 4.90: 29084 Nonbonded interactions: 67325 Sorted by model distance: nonbonded pdb=" OH TYR A 173 " pdb=" OD2 ASP A 198 " model vdw 2.100 3.040 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.183 3.040 nonbonded pdb=" O ALA A 44 " pdb=" OG SER A 47 " model vdw 2.187 3.040 nonbonded pdb=" OG SER R 103 " pdb=" OG SER R 194 " model vdw 2.200 3.040 nonbonded pdb=" O TYR A 173 " pdb=" NH1 ARG A 191 " model vdw 2.202 3.120 ... (remaining 67320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.180 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.620 ------------------------------------------------------------------------------- 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 8518 Z= 0.214 Angle : 0.593 10.023 11549 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 *********************** 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 fitting. 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: 0.2589 time to fit residues: 77.2952 Evaluate side-chains 225 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8518 Z= 0.213 Angle : 0.541 7.436 11549 Z= 0.296 Chirality : 0.043 0.191 1312 Planarity : 0.005 0.072 1456 Dihedral : 8.294 151.923 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 : 7.91 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 *********************** 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 fitting. rotamer outliers: 15 poor density : 249 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8068 (p90) cc_final: 0.7765 (p90) REVERT: A 129 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8267 (ttpp) REVERT: A 188 ARG cc_start: 0.8063 (mtm180) cc_final: 0.7738 (mtm-85) REVERT: A 226 ASN cc_start: 0.8046 (m110) cc_final: 0.7719 (m-40) REVERT: A 232 ASP cc_start: 0.7204 (m-30) cc_final: 0.6964 (m-30) REVERT: B 8 ARG cc_start: 0.7831 (ttt180) cc_final: 0.7565 (ttt180) REVERT: B 13 GLN cc_start: 0.7983 (tp40) cc_final: 0.7091 (tp40) REVERT: B 45 MET cc_start: 0.8495 (mtp) cc_final: 0.8262 (mtp) REVERT: B 134 ARG cc_start: 0.7495 (ptp-110) cc_final: 0.7248 (ptp90) REVERT: B 264 TYR cc_start: 0.8440 (m-80) cc_final: 0.7966 (m-80) REVERT: G 19 LEU cc_start: 0.8340 (mm) cc_final: 0.8130 (mm) REVERT: N 14 GLN cc_start: 0.7356 (mm-40) cc_final: 0.7104 (mm110) REVERT: N 32 ASN cc_start: 0.8502 (m-40) cc_final: 0.8257 (m110) REVERT: N 53 SER cc_start: 0.8322 (t) cc_final: 0.7989 (p) REVERT: N 61 TYR cc_start: 0.8262 (m-80) cc_final: 0.7749 (m-80) REVERT: N 121 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7220 (mm-40) REVERT: R 149 MET cc_start: 0.5441 (tpt) cc_final: 0.5192 (tpt) REVERT: R 181 ILE cc_start: 0.7620 (mm) cc_final: 0.7365 (mm) REVERT: R 182 LEU cc_start: 0.8259 (tp) cc_final: 0.8044 (tt) REVERT: R 193 ILE cc_start: 0.7869 (tp) cc_final: 0.7637 (tp) REVERT: R 222 LYS cc_start: 0.7364 (tmtt) cc_final: 0.7063 (tmtt) REVERT: R 280 ILE cc_start: 0.8666 (mt) cc_final: 0.8440 (mm) REVERT: R 285 LYS cc_start: 0.8547 (pptt) cc_final: 0.8334 (pptt) outliers start: 15 outliers final: 13 residues processed: 249 average time/residue: 0.2560 time to fit residues: 81.5475 Evaluate side-chains 248 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 235 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 51 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 119 ASN B 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8518 Z= 0.226 Angle : 0.530 8.506 11549 Z= 0.286 Chirality : 0.042 0.185 1312 Planarity : 0.004 0.059 1456 Dihedral : 7.858 143.223 1193 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.42 % Allowed : 10.88 % Favored : 86.70 % 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: 1.86 (0.26), residues: 1037 helix: 2.81 (0.23), residues: 440 sheet: 0.77 (0.33), residues: 234 loop : -0.45 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 66 HIS 0.004 0.001 HIS A 212 PHE 0.016 0.001 PHE R 188 TYR 0.022 0.001 TYR B 59 ARG 0.003 0.000 ARG A 120 *********************** 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 269 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 247 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8179 (p90) cc_final: 0.7846 (p90) REVERT: A 129 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8260 (ttpp) REVERT: A 169 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6699 (mm-30) REVERT: A 185 GLU cc_start: 0.6492 (pt0) cc_final: 0.6072 (pt0) REVERT: A 190 THR cc_start: 0.8117 (t) cc_final: 0.7742 (p) REVERT: A 226 ASN cc_start: 0.8033 (m110) cc_final: 0.7716 (m-40) REVERT: A 232 ASP cc_start: 0.7247 (m-30) cc_final: 0.6978 (m-30) REVERT: B 8 ARG cc_start: 0.7813 (ttt180) cc_final: 0.7587 (ttt180) REVERT: B 13 GLN cc_start: 0.7986 (tp40) cc_final: 0.7091 (tp40) REVERT: B 134 ARG cc_start: 0.7487 (ptp-110) cc_final: 0.7231 (ptp90) REVERT: N 14 GLN cc_start: 0.7366 (mm-40) cc_final: 0.7038 (mm-40) REVERT: N 32 ASN cc_start: 0.8467 (m-40) cc_final: 0.8213 (m110) REVERT: N 53 SER cc_start: 0.8328 (t) cc_final: 0.7981 (p) REVERT: N 61 TYR cc_start: 0.8260 (m-80) cc_final: 0.7715 (m-80) REVERT: R 149 MET cc_start: 0.5408 (tpt) cc_final: 0.5159 (tpt) REVERT: R 181 ILE cc_start: 0.7696 (mm) cc_final: 0.7422 (mm) REVERT: R 193 ILE cc_start: 0.7845 (tp) cc_final: 0.7593 (tp) REVERT: R 222 LYS cc_start: 0.7365 (tmtt) cc_final: 0.7036 (tmtt) outliers start: 22 outliers final: 16 residues processed: 250 average time/residue: 0.2519 time to fit residues: 80.5977 Evaluate side-chains 261 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 245 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.0670 chunk 44 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8518 Z= 0.186 Angle : 0.520 10.804 11549 Z= 0.275 Chirality : 0.040 0.146 1312 Planarity : 0.004 0.053 1456 Dihedral : 6.360 123.242 1193 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 3.19 % Allowed : 12.75 % Favored : 84.07 % 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: 1.82 (0.26), residues: 1037 helix: 2.84 (0.23), residues: 440 sheet: 0.63 (0.33), residues: 236 loop : -0.46 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 66 HIS 0.003 0.001 HIS A 212 PHE 0.018 0.001 PHE R 188 TYR 0.016 0.001 TYR B 59 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 251 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7072 (t0) cc_final: 0.6597 (t0) REVERT: A 87 PHE cc_start: 0.8244 (p90) cc_final: 0.7862 (p90) REVERT: A 169 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6676 (mm-30) REVERT: A 226 ASN cc_start: 0.7998 (m110) cc_final: 0.7681 (m-40) REVERT: A 232 ASP cc_start: 0.7240 (m-30) cc_final: 0.6985 (m-30) REVERT: B 8 ARG cc_start: 0.7800 (ttt180) cc_final: 0.7560 (ttt180) REVERT: B 13 GLN cc_start: 0.7976 (tp40) cc_final: 0.7087 (tp40) REVERT: B 134 ARG cc_start: 0.7494 (ptp-110) cc_final: 0.7294 (ptp90) REVERT: B 212 ASP cc_start: 0.7543 (t0) cc_final: 0.7221 (t0) REVERT: N 14 GLN cc_start: 0.7381 (mm-40) cc_final: 0.7081 (mm-40) REVERT: N 32 ASN cc_start: 0.8416 (m-40) cc_final: 0.8164 (m110) REVERT: N 53 SER cc_start: 0.8341 (t) cc_final: 0.7946 (p) REVERT: N 61 TYR cc_start: 0.8262 (m-80) cc_final: 0.7771 (m-80) REVERT: R 26 PHE cc_start: 0.7995 (t80) cc_final: 0.7688 (t80) REVERT: R 149 MET cc_start: 0.5361 (tpt) cc_final: 0.5065 (tpt) REVERT: R 181 ILE cc_start: 0.7679 (mm) cc_final: 0.7395 (mm) REVERT: R 193 ILE cc_start: 0.7868 (tp) cc_final: 0.7622 (tp) REVERT: R 222 LYS cc_start: 0.7333 (tmtt) cc_final: 0.6985 (tmtt) outliers start: 29 outliers final: 20 residues processed: 259 average time/residue: 0.2551 time to fit residues: 84.8588 Evaluate side-chains 263 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 243 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.0870 chunk 56 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 89 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 119 ASN B 155 ASN R 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8518 Z= 0.198 Angle : 0.515 6.573 11549 Z= 0.275 Chirality : 0.041 0.205 1312 Planarity : 0.004 0.049 1456 Dihedral : 4.214 20.336 1193 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.70 % Favored : 97.20 % Rotamer: Outliers : 3.19 % Allowed : 14.29 % Favored : 82.53 % 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: 1.74 (0.26), residues: 1037 helix: 2.79 (0.23), residues: 440 sheet: 0.52 (0.33), residues: 234 loop : -0.48 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 66 HIS 0.003 0.001 HIS A 212 PHE 0.017 0.001 PHE R 188 TYR 0.015 0.001 TYR B 59 ARG 0.003 0.000 ARG A 38 *********************** 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 287 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 258 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7064 (t0) cc_final: 0.6600 (t0) REVERT: A 87 PHE cc_start: 0.8291 (p90) cc_final: 0.7862 (p90) REVERT: A 122 GLN cc_start: 0.8219 (tp-100) cc_final: 0.7957 (tp-100) REVERT: A 169 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6664 (mm-30) REVERT: A 198 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6509 (t0) REVERT: A 226 ASN cc_start: 0.8007 (m110) cc_final: 0.7685 (m-40) REVERT: A 232 ASP cc_start: 0.7246 (m-30) cc_final: 0.6994 (m-30) REVERT: B 8 ARG cc_start: 0.7805 (ttt180) cc_final: 0.7540 (ttt180) REVERT: B 13 GLN cc_start: 0.7984 (tp40) cc_final: 0.7093 (tp40) REVERT: B 74 SER cc_start: 0.8130 (t) cc_final: 0.7752 (p) REVERT: B 134 ARG cc_start: 0.7501 (ptp-110) cc_final: 0.7266 (ptp90) REVERT: N 14 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7132 (mm-40) REVERT: N 32 ASN cc_start: 0.8388 (m-40) cc_final: 0.8138 (m110) REVERT: N 53 SER cc_start: 0.8354 (t) cc_final: 0.7966 (p) REVERT: N 61 TYR cc_start: 0.8273 (m-80) cc_final: 0.7741 (m-80) REVERT: R 26 PHE cc_start: 0.7980 (t80) cc_final: 0.7698 (t80) REVERT: R 149 MET cc_start: 0.5440 (tpt) cc_final: 0.5128 (tpt) REVERT: R 181 ILE cc_start: 0.7717 (mm) cc_final: 0.7489 (mm) REVERT: R 193 ILE cc_start: 0.7872 (tp) cc_final: 0.7633 (tp) REVERT: R 222 LYS cc_start: 0.7325 (tmtt) cc_final: 0.6970 (tmtt) outliers start: 29 outliers final: 16 residues processed: 263 average time/residue: 0.2513 time to fit residues: 84.7841 Evaluate side-chains 272 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 255 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 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 104 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 119 ASN B 155 ASN R 31 ASN R 224 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8518 Z= 0.207 Angle : 0.530 9.248 11549 Z= 0.280 Chirality : 0.041 0.152 1312 Planarity : 0.004 0.045 1456 Dihedral : 4.155 20.303 1193 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.70 % Favored : 97.20 % Rotamer: Outliers : 3.08 % Allowed : 15.93 % Favored : 80.99 % 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: 1.73 (0.26), residues: 1037 helix: 2.79 (0.23), residues: 440 sheet: 0.52 (0.33), residues: 232 loop : -0.50 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 66 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 0.003 0.000 ARG A 38 *********************** 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 fitting. rotamer outliers: 28 poor density : 260 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7084 (t0) cc_final: 0.6621 (t0) REVERT: A 87 PHE cc_start: 0.8326 (p90) cc_final: 0.7883 (p90) REVERT: A 122 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7944 (tp-100) REVERT: A 169 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6556 (mm-30) REVERT: A 198 ASP cc_start: 0.6928 (OUTLIER) cc_final: 0.6531 (t0) REVERT: A 226 ASN cc_start: 0.8037 (m110) cc_final: 0.7704 (m-40) REVERT: A 232 ASP cc_start: 0.7278 (m-30) cc_final: 0.7028 (m-30) REVERT: B 8 ARG cc_start: 0.7807 (ttt180) cc_final: 0.7539 (ttt180) REVERT: B 13 GLN cc_start: 0.7988 (tp40) cc_final: 0.7096 (tp40) REVERT: B 61 MET cc_start: 0.7300 (ppp) cc_final: 0.7090 (ppp) REVERT: B 74 SER cc_start: 0.8111 (t) cc_final: 0.7747 (p) REVERT: B 134 ARG cc_start: 0.7505 (ptp-110) cc_final: 0.7264 (ptp90) REVERT: N 14 GLN cc_start: 0.7372 (mm-40) cc_final: 0.7113 (mm-40) REVERT: N 32 ASN cc_start: 0.8385 (m-40) cc_final: 0.8133 (m110) REVERT: N 53 SER cc_start: 0.8358 (t) cc_final: 0.7978 (p) REVERT: N 61 TYR cc_start: 0.8272 (m-80) cc_final: 0.7723 (m-80) REVERT: R 26 PHE cc_start: 0.7979 (t80) cc_final: 0.7605 (t80) REVERT: R 149 MET cc_start: 0.5473 (tpt) cc_final: 0.5151 (tpt) REVERT: R 181 ILE cc_start: 0.7723 (mm) cc_final: 0.7507 (mm) REVERT: R 193 ILE cc_start: 0.7872 (tp) cc_final: 0.7629 (tp) REVERT: R 222 LYS cc_start: 0.7347 (tmtt) cc_final: 0.6979 (tmtt) outliers start: 28 outliers final: 25 residues processed: 264 average time/residue: 0.2531 time to fit residues: 85.8241 Evaluate side-chains 281 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 255 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 185 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain N residue 36 ASN Chi-restraints excluded: chain N residue 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 104 ILE Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.8980 chunk 11 optimal weight: 0.0010 chunk 56 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 45 optimal weight: 0.0570 chunk 61 optimal weight: 0.8980 overall best weight: 0.4504 ------------------------------------------------------------------------------- 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 119 ASN B 155 ASN R 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8518 Z= 0.169 Angle : 0.509 7.148 11549 Z= 0.269 Chirality : 0.040 0.148 1312 Planarity : 0.004 0.043 1456 Dihedral : 4.069 19.579 1193 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.41 % Favored : 97.49 % Rotamer: Outliers : 3.41 % Allowed : 16.81 % Favored : 79.78 % 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: 2.85 (0.23), residues: 440 sheet: 0.50 (0.33), residues: 232 loop : -0.46 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 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 B 59 ARG 0.004 0.000 ARG A 38 *********************** 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 278 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 247 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7086 (t0) cc_final: 0.6599 (t0) REVERT: A 87 PHE cc_start: 0.8360 (p90) cc_final: 0.7922 (p90) REVERT: A 122 GLN cc_start: 0.8205 (tp-100) cc_final: 0.7976 (tp40) REVERT: A 134 ASN cc_start: 0.7395 (OUTLIER) cc_final: 0.7041 (m-40) REVERT: A 169 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6527 (mm-30) REVERT: A 198 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6500 (t0) REVERT: A 232 ASP cc_start: 0.7244 (m-30) cc_final: 0.6995 (m-30) REVERT: A 236 ASP cc_start: 0.7797 (t0) cc_final: 0.7335 (t70) REVERT: A 240 LYS cc_start: 0.8340 (mmtm) cc_final: 0.7879 (mptt) REVERT: B 8 ARG cc_start: 0.7795 (ttt180) cc_final: 0.7516 (ttt180) REVERT: B 13 GLN cc_start: 0.7979 (tp40) cc_final: 0.7092 (tp40) REVERT: B 74 SER cc_start: 0.8101 (t) cc_final: 0.7728 (p) REVERT: B 134 ARG cc_start: 0.7518 (ptp-110) cc_final: 0.7288 (ptp90) REVERT: B 204 CYS cc_start: 0.7150 (m) cc_final: 0.6884 (m) REVERT: N 14 GLN cc_start: 0.7362 (mm-40) cc_final: 0.7104 (mm-40) REVERT: N 32 ASN cc_start: 0.8318 (m-40) cc_final: 0.8082 (m110) REVERT: N 61 TYR cc_start: 0.8264 (m-80) cc_final: 0.7712 (m-80) REVERT: N 109 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.6272 (m-80) REVERT: R 26 PHE cc_start: 0.7911 (t80) cc_final: 0.7700 (t80) REVERT: R 106 TYR cc_start: 0.8060 (m-10) cc_final: 0.7823 (m-10) REVERT: R 149 MET cc_start: 0.5375 (tpt) cc_final: 0.5078 (tpt) REVERT: R 181 ILE cc_start: 0.7730 (mm) cc_final: 0.7495 (mm) REVERT: R 193 ILE cc_start: 0.7753 (tp) cc_final: 0.7522 (tp) outliers start: 31 outliers final: 26 residues processed: 255 average time/residue: 0.2516 time to fit residues: 82.4402 Evaluate side-chains 274 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 245 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 134 ASN Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 36 ASN Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 chunk 67 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8518 Z= 0.231 Angle : 0.538 6.539 11549 Z= 0.285 Chirality : 0.041 0.151 1312 Planarity : 0.004 0.043 1456 Dihedral : 4.155 19.914 1193 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.01 % Rotamer: Outliers : 3.19 % Allowed : 16.81 % Favored : 80.00 % 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: 1.70 (0.26), residues: 1037 helix: 2.73 (0.23), residues: 442 sheet: 0.53 (0.32), residues: 230 loop : -0.48 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 300 HIS 0.003 0.001 HIS R 205 PHE 0.016 0.001 PHE R 188 TYR 0.017 0.001 TYR B 59 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 247 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7097 (t0) cc_final: 0.6626 (t0) REVERT: A 87 PHE cc_start: 0.8376 (p90) cc_final: 0.7905 (p90) REVERT: A 120 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6877 (mtm-85) REVERT: A 122 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7950 (tp40) REVERT: A 169 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6535 (mm-30) REVERT: A 198 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6554 (t0) REVERT: A 232 ASP cc_start: 0.7293 (m-30) cc_final: 0.7047 (m-30) REVERT: A 236 ASP cc_start: 0.7812 (t0) cc_final: 0.7505 (t0) REVERT: B 8 ARG cc_start: 0.7809 (ttt180) cc_final: 0.7517 (ttt180) REVERT: B 13 GLN cc_start: 0.7985 (tp40) cc_final: 0.7099 (tp40) REVERT: B 74 SER cc_start: 0.8075 (t) cc_final: 0.7718 (p) REVERT: B 134 ARG cc_start: 0.7513 (ptp-110) cc_final: 0.7306 (ptp90) REVERT: B 204 CYS cc_start: 0.7228 (m) cc_final: 0.7000 (m) REVERT: N 14 GLN cc_start: 0.7359 (mm-40) cc_final: 0.7103 (mm-40) REVERT: N 32 ASN cc_start: 0.8340 (m-40) cc_final: 0.8109 (m110) REVERT: N 61 TYR cc_start: 0.8278 (m-80) cc_final: 0.7728 (m-80) REVERT: N 109 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.6600 (m-80) REVERT: R 26 PHE cc_start: 0.7959 (t80) cc_final: 0.7610 (t80) REVERT: R 149 MET cc_start: 0.5414 (tpt) cc_final: 0.5104 (tpt) REVERT: R 181 ILE cc_start: 0.7764 (mm) cc_final: 0.7562 (mm) REVERT: R 193 ILE cc_start: 0.7856 (tp) cc_final: 0.7614 (tp) REVERT: R 222 LYS cc_start: 0.7401 (tmtt) cc_final: 0.6990 (tmtt) REVERT: R 284 LYS cc_start: 0.7581 (ttmt) cc_final: 0.7275 (ttmt) outliers start: 29 outliers final: 25 residues processed: 253 average time/residue: 0.2629 time to fit residues: 85.2817 Evaluate side-chains 276 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 248 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 185 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 36 ASN Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 0.0020 chunk 60 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8518 Z= 0.196 Angle : 0.530 8.235 11549 Z= 0.280 Chirality : 0.041 0.150 1312 Planarity : 0.004 0.043 1456 Dihedral : 4.117 19.524 1193 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.51 % Favored : 97.40 % Rotamer: Outliers : 3.19 % Allowed : 17.25 % 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: 1.76 (0.26), residues: 1037 helix: 2.76 (0.23), residues: 442 sheet: 0.58 (0.32), residues: 228 loop : -0.43 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 300 HIS 0.003 0.001 HIS A 85 PHE 0.017 0.001 PHE R 188 TYR 0.015 0.001 TYR B 59 ARG 0.004 0.000 ARG A 38 *********************** 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 274 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 245 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7086 (t0) cc_final: 0.6608 (t0) REVERT: A 87 PHE cc_start: 0.8362 (p90) cc_final: 0.7841 (p90) REVERT: A 120 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6946 (mtm-85) REVERT: A 122 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7921 (tp40) REVERT: A 169 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6676 (mm-30) REVERT: A 198 ASP cc_start: 0.6910 (OUTLIER) cc_final: 0.6556 (t0) REVERT: A 232 ASP cc_start: 0.7332 (m-30) cc_final: 0.7049 (m-30) REVERT: A 236 ASP cc_start: 0.7811 (t0) cc_final: 0.7524 (t70) REVERT: B 8 ARG cc_start: 0.7810 (ttt180) cc_final: 0.7509 (ttt180) REVERT: B 13 GLN cc_start: 0.7980 (tp40) cc_final: 0.7099 (tp40) REVERT: B 74 SER cc_start: 0.8062 (t) cc_final: 0.7704 (p) REVERT: B 204 CYS cc_start: 0.7162 (m) cc_final: 0.6943 (m) REVERT: N 14 GLN cc_start: 0.7386 (mm-40) cc_final: 0.7128 (mm-40) REVERT: N 32 ASN cc_start: 0.8282 (m-40) cc_final: 0.8064 (m110) REVERT: N 61 TYR cc_start: 0.8275 (m-80) cc_final: 0.7723 (m-80) REVERT: N 109 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.6524 (m-80) REVERT: R 26 PHE cc_start: 0.7915 (t80) cc_final: 0.7715 (t80) REVERT: R 149 MET cc_start: 0.5373 (tpt) cc_final: 0.5067 (tpt) REVERT: R 181 ILE cc_start: 0.7753 (mm) cc_final: 0.7537 (mm) REVERT: R 193 ILE cc_start: 0.7844 (tp) cc_final: 0.7605 (tp) REVERT: R 222 LYS cc_start: 0.7382 (tmtt) cc_final: 0.6986 (tmtt) outliers start: 29 outliers final: 25 residues processed: 251 average time/residue: 0.2570 time to fit residues: 82.4715 Evaluate side-chains 271 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 243 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 185 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 36 ASN Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 94 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 119 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8518 Z= 0.214 Angle : 0.542 8.231 11549 Z= 0.285 Chirality : 0.041 0.151 1312 Planarity : 0.004 0.043 1456 Dihedral : 4.145 19.708 1193 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.01 % Rotamer: Outliers : 2.86 % Allowed : 17.69 % Favored : 79.45 % 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: 1.73 (0.26), residues: 1037 helix: 2.73 (0.23), residues: 441 sheet: 0.51 (0.32), residues: 228 loop : -0.40 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 300 HIS 0.003 0.001 HIS A 212 PHE 0.016 0.001 PHE R 188 TYR 0.016 0.001 TYR B 59 ARG 0.004 0.000 ARG A 38 ********************** 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 fitting. rotamer outliers: 26 poor density : 241 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7087 (t0) cc_final: 0.6623 (t0) REVERT: A 87 PHE cc_start: 0.8362 (p90) cc_final: 0.7833 (p90) REVERT: A 122 GLN cc_start: 0.8164 (tp-100) cc_final: 0.7909 (tp40) REVERT: A 169 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6712 (mm-30) REVERT: A 198 ASP cc_start: 0.6917 (t0) cc_final: 0.6565 (t0) REVERT: A 232 ASP cc_start: 0.7338 (m-30) cc_final: 0.7047 (m-30) REVERT: B 8 ARG cc_start: 0.7815 (ttt180) cc_final: 0.7514 (ttt180) REVERT: B 13 GLN cc_start: 0.7986 (tp40) cc_final: 0.7104 (tp40) REVERT: B 74 SER cc_start: 0.8064 (t) cc_final: 0.7722 (p) REVERT: B 204 CYS cc_start: 0.7223 (m) cc_final: 0.6995 (m) REVERT: B 325 MET cc_start: 0.7252 (mtp) cc_final: 0.7046 (mtp) REVERT: N 14 GLN cc_start: 0.7361 (mm-40) cc_final: 0.7109 (mm-40) REVERT: N 32 ASN cc_start: 0.8274 (m-40) cc_final: 0.8038 (m110) REVERT: N 61 TYR cc_start: 0.8273 (m-80) cc_final: 0.7783 (m-80) REVERT: N 109 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.6493 (m-80) REVERT: R 149 MET cc_start: 0.5378 (tpt) cc_final: 0.5073 (tpt) REVERT: R 193 ILE cc_start: 0.7902 (tp) cc_final: 0.7668 (tp) REVERT: R 222 LYS cc_start: 0.7432 (tmtt) cc_final: 0.7032 (tmtt) outliers start: 26 outliers final: 22 residues processed: 246 average time/residue: 0.2549 time to fit residues: 81.0815 Evaluate side-chains 264 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 241 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 185 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 N residue 36 ASN Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 155 ASN R 31 ASN ** R 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.144607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.125987 restraints weight = 12391.647| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.27 r_work: 0.3514 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8518 Z= 0.186 Angle : 0.551 9.103 11549 Z= 0.286 Chirality : 0.042 0.206 1312 Planarity : 0.004 0.043 1456 Dihedral : 4.103 19.336 1193 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.30 % Rotamer: Outliers : 2.86 % Allowed : 18.57 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.71 (0.26), residues: 1037 helix: 2.74 (0.23), residues: 441 sheet: 0.53 (0.33), residues: 210 loop : -0.44 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 300 HIS 0.003 0.001 HIS A 85 PHE 0.017 0.001 PHE R 188 TYR 0.023 0.001 TYR R 106 ARG 0.004 0.000 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2407.10 seconds wall clock time: 43 minutes 14.35 seconds (2594.35 seconds total)