Starting phenix.real_space_refine on Tue Sep 24 15:41:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/09_2024/6k41_9911.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/09_2024/6k41_9911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/09_2024/6k41_9911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/09_2024/6k41_9911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/09_2024/6k41_9911.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/09_2024/6k41_9911.cif" } resolution = 2.9 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= 0.000 sd= 0.003 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 55 5.16 5 C 5384 2.51 5 N 1435 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8430 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain breaks: 3 Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2559 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "R" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1952 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain breaks: 5 Chain: "H" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1793 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CZX': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 6.32, per 1000 atoms: 0.75 Number of scatterers: 8430 At special positions: 0 Unit cell: (109.1, 110.191, 119.464, 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 55 16.00 O 1556 8.00 N 1435 7.00 C 5384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " 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: 2.23 Conformation dependent library (CDL) restraints added in 963.0 milliseconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 36.5% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.536A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.341A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.514A pdb=" N GLU A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 9 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.560A 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 'G' and resid 45 through 48 Processing helix chain 'R' and resid 12 through 39 Processing helix chain 'R' and resid 48 through 74 removed outlier: 3.734A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) Proline residue: R 67 - end of helix Processing helix chain 'R' and resid 86 through 116 Processing helix chain 'R' and resid 116 through 122 removed outlier: 3.680A pdb=" N SER R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 145 Processing helix chain 'R' and resid 171 through 181 removed outlier: 3.630A pdb=" N ALA R 175 " --> pdb=" O TRP R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 203 Processing helix chain 'R' and resid 362 through 393 removed outlier: 3.538A pdb=" N LYS R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE R 380 " --> pdb=" O VAL R 376 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL R 381 " --> pdb=" O ILE R 377 " (cutoff:3.500A) Proline residue: R 386 - end of helix Processing helix chain 'R' and resid 406 through 428 removed outlier: 3.802A pdb=" N TYR R 416 " --> pdb=" O PHE R 412 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN R 418 " --> pdb=" O ILE R 414 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 430 through 442 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.508A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.850A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.304A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.507A 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: 3.871A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.597A 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: 6.785A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.739A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.859A 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: 6.845A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.648A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.591A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.785A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.219A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 128 through 129 removed outlier: 3.765A pdb=" N ALA H 199 " --> pdb=" O SER H 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 134 through 137 removed outlier: 3.826A pdb=" N GLU H 234 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 137 " --> pdb=" O GLU H 234 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY H 213 " --> pdb=" O LEU H 233 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP H 164 " --> pdb=" O LEU H 176 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1185 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: 2.50 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2170 1.33 - 1.45: 1760 1.45 - 1.57: 4598 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 8603 Sorted by residual: bond pdb=" C09 CZX R 501 " pdb=" C12 CZX R 501 " ideal model delta sigma weight residual 1.385 1.523 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C11 CZX R 501 " pdb=" C12 CZX R 501 " ideal model delta sigma weight residual 1.386 1.522 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C08 CZX R 501 " pdb=" C11 CZX R 501 " ideal model delta sigma weight residual 1.392 1.526 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C04 CZX R 501 " pdb=" C09 CZX R 501 " ideal model delta sigma weight residual 1.393 1.521 -0.128 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C04 CZX R 501 " pdb=" C05 CZX R 501 " ideal model delta sigma weight residual 1.403 1.531 -0.128 2.00e-02 2.50e+03 4.08e+01 ... (remaining 8598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 11397 3.08 - 6.16: 226 6.16 - 9.24: 20 9.24 - 12.32: 3 12.32 - 15.40: 4 Bond angle restraints: 11650 Sorted by residual: angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 113.71 107.35 6.36 9.50e-01 1.11e+00 4.49e+01 angle pdb=" N LEU R 145 " pdb=" CA LEU R 145 " pdb=" C LEU R 145 " ideal model delta sigma weight residual 109.81 122.76 -12.95 2.21e+00 2.05e-01 3.44e+01 angle pdb=" N PRO R 146 " pdb=" CA PRO R 146 " pdb=" C PRO R 146 " ideal model delta sigma weight residual 110.70 116.69 -5.99 1.22e+00 6.72e-01 2.41e+01 angle pdb=" C ARG H 179 " pdb=" N MET H 180 " pdb=" CA MET H 180 " ideal model delta sigma weight residual 121.54 129.81 -8.27 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C THR A 296 " pdb=" N TYR A 297 " pdb=" CA TYR A 297 " ideal model delta sigma weight residual 120.54 126.25 -5.71 1.35e+00 5.49e-01 1.79e+01 ... (remaining 11645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 4822 16.48 - 32.95: 219 32.95 - 49.43: 41 49.43 - 65.90: 2 65.90 - 82.38: 6 Dihedral angle restraints: 5090 sinusoidal: 1972 harmonic: 3118 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 164 " pdb=" CB CYS R 164 " ideal model delta sinusoidal sigma weight residual -86.00 -168.38 82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CA SER B 281 " pdb=" C SER B 281 " pdb=" N GLY B 282 " pdb=" CA GLY B 282 " ideal model delta harmonic sigma weight residual 180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ARG R 116 " pdb=" C ARG R 116 " pdb=" N ALA R 117 " pdb=" CA ALA R 117 " ideal model delta harmonic sigma weight residual -180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 5087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1142 0.087 - 0.174: 169 0.174 - 0.260: 13 0.260 - 0.347: 3 0.347 - 0.434: 1 Chirality restraints: 1328 Sorted by residual: chirality pdb=" CB VAL B 71 " pdb=" CA VAL B 71 " pdb=" CG1 VAL B 71 " pdb=" CG2 VAL B 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CG LEU G 50 " pdb=" CB LEU G 50 " pdb=" CD1 LEU G 50 " pdb=" CD2 LEU G 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB VAL A 219 " pdb=" CA VAL A 219 " pdb=" CG1 VAL A 219 " pdb=" CG2 VAL A 219 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 1325 not shown) Planarity restraints: 1467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 62 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C ALA R 62 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA R 62 " -0.018 2.00e-02 2.50e+03 pdb=" N THR R 63 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 111 " 0.019 2.00e-02 2.50e+03 1.72e-02 7.43e+00 pdb=" CG TRP H 111 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP H 111 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP H 111 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP H 111 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 111 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 111 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 111 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 111 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 111 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 50 " -0.019 2.00e-02 2.50e+03 1.94e-02 6.60e+00 pdb=" CG PHE R 50 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE R 50 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE R 50 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE R 50 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE R 50 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE R 50 " -0.001 2.00e-02 2.50e+03 ... (remaining 1464 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 304 2.71 - 3.26: 7545 3.26 - 3.81: 13439 3.81 - 4.35: 17722 4.35 - 4.90: 29880 Nonbonded interactions: 68890 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.166 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.189 3.040 nonbonded pdb=" OG SER R 69 " pdb=" OH TYR R 88 " model vdw 2.220 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.243 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR H 163 " model vdw 2.244 3.040 ... (remaining 68885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 10.550 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: 0.000 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.560 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.009 0.138 8603 Z= 0.564 Angle : 1.065 15.404 11650 Z= 0.571 Chirality : 0.062 0.434 1328 Planarity : 0.007 0.062 1467 Dihedral : 10.212 74.612 3065 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.44 % Allowed : 3.40 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: -2.62 (0.22), residues: 1049 helix: -1.40 (0.22), residues: 365 sheet: -0.89 (0.30), residues: 277 loop : -2.54 (0.25), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP H 111 HIS 0.014 0.004 HIS B 62 PHE 0.044 0.004 PHE R 50 TYR 0.030 0.004 TYR B 59 ARG 0.019 0.002 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 208 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7554 (m-30) cc_final: 0.7321 (m-30) REVERT: A 193 LYS cc_start: 0.7468 (mtpm) cc_final: 0.7179 (mmpt) REVERT: A 210 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7678 (mmtm) REVERT: A 328 ASP cc_start: 0.7295 (m-30) cc_final: 0.6547 (m-30) REVERT: A 332 ILE cc_start: 0.8282 (mp) cc_final: 0.8001 (mt) REVERT: B 207 SER cc_start: 0.8695 (p) cc_final: 0.8379 (m) REVERT: G 19 LEU cc_start: 0.8030 (mt) cc_final: 0.7745 (mp) REVERT: R 72 ASN cc_start: 0.6408 (t0) cc_final: 0.6057 (t0) REVERT: R 201 ARG cc_start: 0.6969 (ttp-170) cc_final: 0.6739 (tmm160) REVERT: R 407 LEU cc_start: 0.6761 (mt) cc_final: 0.6501 (mm) REVERT: H 3 GLN cc_start: 0.7505 (mt0) cc_final: 0.7304 (mm-40) outliers start: 4 outliers final: 2 residues processed: 212 average time/residue: 1.2679 time to fit residues: 284.1614 Evaluate side-chains 135 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 214 HIS A 257 ASN B 32 GLN B 239 ASN B 293 ASN R 30 ASN H 167 GLN H 171 GLN H 219 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8603 Z= 0.242 Angle : 0.625 9.132 11650 Z= 0.335 Chirality : 0.045 0.157 1328 Planarity : 0.005 0.048 1467 Dihedral : 5.473 42.447 1173 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.27 % Allowed : 10.62 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: -0.88 (0.25), residues: 1049 helix: 0.83 (0.27), residues: 361 sheet: -0.39 (0.30), residues: 284 loop : -2.03 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.008 0.002 HIS B 62 PHE 0.038 0.002 PHE R 369 TYR 0.026 0.002 TYR B 105 ARG 0.007 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 146 time to evaluate : 0.969 Fit side-chains REVERT: A 193 LYS cc_start: 0.7502 (mtpm) cc_final: 0.7149 (mmpt) REVERT: A 210 LYS cc_start: 0.8249 (ttmm) cc_final: 0.7790 (mmtm) REVERT: A 277 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6886 (mm-30) REVERT: A 308 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: A 328 ASP cc_start: 0.7360 (m-30) cc_final: 0.6549 (m-30) REVERT: B 45 MET cc_start: 0.8309 (mtt) cc_final: 0.7832 (mtt) REVERT: B 212 ASP cc_start: 0.7533 (t0) cc_final: 0.7205 (t0) REVERT: R 72 ASN cc_start: 0.6503 (t0) cc_final: 0.6247 (t0) REVERT: R 127 ARG cc_start: 0.7107 (ptm160) cc_final: 0.6693 (ptt90) REVERT: R 187 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8374 (mm) REVERT: R 201 ARG cc_start: 0.7125 (ttp-170) cc_final: 0.6777 (ttm110) REVERT: R 377 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8135 (tp) REVERT: H 87 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6934 (mtm180) outliers start: 39 outliers final: 12 residues processed: 166 average time/residue: 1.3130 time to fit residues: 230.8682 Evaluate side-chains 151 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 377 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 143 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN H 130 GLN H 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8603 Z= 0.176 Angle : 0.549 7.798 11650 Z= 0.294 Chirality : 0.042 0.147 1328 Planarity : 0.004 0.043 1467 Dihedral : 4.942 37.144 1173 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.18 % Allowed : 13.58 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: -0.13 (0.26), residues: 1049 helix: 1.70 (0.28), residues: 359 sheet: -0.23 (0.30), residues: 292 loop : -1.64 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.034 0.002 PHE R 369 TYR 0.014 0.002 TYR B 105 ARG 0.006 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7796 (mtmt) REVERT: A 193 LYS cc_start: 0.7534 (mtpm) cc_final: 0.7210 (mmpt) REVERT: A 210 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7781 (mmtm) REVERT: A 277 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: A 308 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: A 328 ASP cc_start: 0.7292 (m-30) cc_final: 0.6433 (m-30) REVERT: B 45 MET cc_start: 0.8325 (mtt) cc_final: 0.7879 (mtt) REVERT: B 212 ASP cc_start: 0.7409 (t0) cc_final: 0.7121 (t0) REVERT: R 27 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7467 (mm) REVERT: R 72 ASN cc_start: 0.6551 (t0) cc_final: 0.6318 (t0) REVERT: R 127 ARG cc_start: 0.7007 (ptm160) cc_final: 0.6610 (ptt90) REVERT: R 187 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8175 (mt) REVERT: R 201 ARG cc_start: 0.7140 (ttp-170) cc_final: 0.6808 (ttm110) outliers start: 29 outliers final: 14 residues processed: 157 average time/residue: 1.3133 time to fit residues: 218.4200 Evaluate side-chains 151 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 428 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 162 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 0.0270 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 64 optimal weight: 0.0970 chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN H 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8603 Z= 0.129 Angle : 0.503 9.151 11650 Z= 0.267 Chirality : 0.041 0.137 1328 Planarity : 0.004 0.038 1467 Dihedral : 4.502 42.918 1172 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.72 % Allowed : 14.57 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.39 (0.26), residues: 1049 helix: 2.16 (0.28), residues: 361 sheet: 0.16 (0.31), residues: 277 loop : -1.45 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.003 0.001 HIS A 189 PHE 0.032 0.001 PHE R 369 TYR 0.013 0.001 TYR H 59 ARG 0.005 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7798 (mtmt) REVERT: A 193 LYS cc_start: 0.7507 (mtpm) cc_final: 0.7203 (mmpt) REVERT: A 210 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7774 (mmtm) REVERT: A 277 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6951 (mm-30) REVERT: A 328 ASP cc_start: 0.7262 (m-30) cc_final: 0.6352 (m-30) REVERT: B 45 MET cc_start: 0.8333 (mtt) cc_final: 0.7889 (mtt) REVERT: B 165 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8410 (m) REVERT: B 212 ASP cc_start: 0.7239 (t0) cc_final: 0.7004 (t0) REVERT: R 27 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7351 (mm) REVERT: R 72 ASN cc_start: 0.6567 (t0) cc_final: 0.6283 (t0) REVERT: R 127 ARG cc_start: 0.6865 (ptm160) cc_final: 0.6478 (ptt90) REVERT: R 187 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8109 (mt) REVERT: R 201 ARG cc_start: 0.7121 (ttp-170) cc_final: 0.6815 (ttm110) outliers start: 34 outliers final: 11 residues processed: 164 average time/residue: 1.2147 time to fit residues: 211.4396 Evaluate side-chains 143 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 162 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN R 30 ASN H 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8603 Z= 0.180 Angle : 0.541 7.483 11650 Z= 0.286 Chirality : 0.042 0.147 1328 Planarity : 0.004 0.039 1467 Dihedral : 4.687 38.689 1172 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.38 % Allowed : 15.01 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.50 (0.26), residues: 1049 helix: 2.24 (0.28), residues: 360 sheet: 0.18 (0.30), residues: 290 loop : -1.37 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.032 0.001 PHE R 369 TYR 0.013 0.001 TYR R 391 ARG 0.007 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8174 (tmmt) REVERT: A 24 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7759 (mtmt) REVERT: A 193 LYS cc_start: 0.7551 (mtpm) cc_final: 0.7204 (mmpt) REVERT: A 210 LYS cc_start: 0.8171 (ttmm) cc_final: 0.7804 (mmtm) REVERT: A 277 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6957 (mm-30) REVERT: A 328 ASP cc_start: 0.7243 (m-30) cc_final: 0.6312 (m-30) REVERT: B 212 ASP cc_start: 0.7304 (t0) cc_final: 0.7046 (t0) REVERT: R 27 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7365 (mm) REVERT: R 72 ASN cc_start: 0.6611 (t0) cc_final: 0.6334 (t0) REVERT: R 187 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8192 (mt) REVERT: R 201 ARG cc_start: 0.7169 (ttp-170) cc_final: 0.6851 (ttm110) REVERT: R 368 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.5415 (ttt90) outliers start: 40 outliers final: 17 residues processed: 159 average time/residue: 1.2744 time to fit residues: 215.0964 Evaluate side-chains 154 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 368 ARG Chi-restraints excluded: chain R residue 428 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 143 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.0770 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 257 ASN A 270 ASN R 30 ASN H 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8603 Z= 0.213 Angle : 0.573 9.944 11650 Z= 0.300 Chirality : 0.043 0.151 1328 Planarity : 0.004 0.040 1467 Dihedral : 4.824 35.424 1172 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.82 % Allowed : 15.01 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.51 (0.26), residues: 1049 helix: 2.16 (0.28), residues: 359 sheet: 0.17 (0.29), residues: 296 loop : -1.27 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.032 0.002 PHE R 369 TYR 0.017 0.002 TYR H 59 ARG 0.008 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 134 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8176 (tmmt) REVERT: A 24 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7781 (mtmt) REVERT: A 193 LYS cc_start: 0.7604 (mtpm) cc_final: 0.7178 (mmpt) REVERT: A 210 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7786 (mmtm) REVERT: A 277 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7055 (mm-30) REVERT: A 323 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7235 (mtm) REVERT: A 328 ASP cc_start: 0.7186 (m-30) cc_final: 0.6279 (m-30) REVERT: B 212 ASP cc_start: 0.7338 (t0) cc_final: 0.7049 (t0) REVERT: R 27 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7342 (mm) REVERT: R 72 ASN cc_start: 0.6598 (t0) cc_final: 0.6350 (t0) REVERT: R 127 ARG cc_start: 0.7132 (ptm160) cc_final: 0.6658 (ptt90) REVERT: R 187 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8294 (mm) REVERT: R 201 ARG cc_start: 0.7161 (ttp-170) cc_final: 0.6843 (ttm110) REVERT: R 368 ARG cc_start: 0.6365 (OUTLIER) cc_final: 0.5436 (ttt90) REVERT: H 87 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6946 (mtt90) REVERT: H 166 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8233 (tp) outliers start: 44 outliers final: 18 residues processed: 160 average time/residue: 1.3218 time to fit residues: 224.0154 Evaluate side-chains 157 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 368 ARG Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 166 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8603 Z= 0.183 Angle : 0.556 10.490 11650 Z= 0.291 Chirality : 0.042 0.146 1328 Planarity : 0.004 0.040 1467 Dihedral : 4.699 36.951 1172 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.60 % Allowed : 15.55 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.61 (0.26), residues: 1049 helix: 2.25 (0.28), residues: 360 sheet: 0.18 (0.29), residues: 298 loop : -1.18 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.031 0.001 PHE R 369 TYR 0.012 0.001 TYR R 391 ARG 0.010 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 134 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8196 (tmmt) REVERT: A 24 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7792 (mtmt) REVERT: A 193 LYS cc_start: 0.7613 (mtpm) cc_final: 0.7176 (mmpt) REVERT: A 210 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7797 (mmtm) REVERT: A 277 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7059 (mm-30) REVERT: A 309 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6914 (mt-10) REVERT: A 328 ASP cc_start: 0.7192 (m-30) cc_final: 0.6285 (m-30) REVERT: B 197 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7480 (mmt180) REVERT: B 212 ASP cc_start: 0.7298 (t0) cc_final: 0.7024 (t0) REVERT: R 27 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7298 (mm) REVERT: R 72 ASN cc_start: 0.6596 (t0) cc_final: 0.6352 (t0) REVERT: R 127 ARG cc_start: 0.7063 (ptm160) cc_final: 0.6595 (ptt90) REVERT: R 187 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8187 (mt) REVERT: R 201 ARG cc_start: 0.7171 (ttp-170) cc_final: 0.6801 (ttm110) REVERT: R 368 ARG cc_start: 0.6361 (OUTLIER) cc_final: 0.5901 (ttt90) REVERT: H 87 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6974 (mtt90) REVERT: H 88 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7946 (m) REVERT: H 166 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8221 (tp) outliers start: 42 outliers final: 20 residues processed: 162 average time/residue: 1.3148 time to fit residues: 225.7421 Evaluate side-chains 158 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 368 ARG Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 0.0980 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 270 ASN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN H 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8603 Z= 0.142 Angle : 0.526 10.539 11650 Z= 0.274 Chirality : 0.041 0.139 1328 Planarity : 0.004 0.040 1467 Dihedral : 4.450 41.438 1172 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.61 % Allowed : 16.43 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.82 (0.26), residues: 1049 helix: 2.46 (0.28), residues: 356 sheet: 0.34 (0.29), residues: 296 loop : -1.11 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS B 62 PHE 0.030 0.001 PHE R 369 TYR 0.014 0.001 TYR H 59 ARG 0.011 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8195 (tmmt) REVERT: A 24 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7769 (mtmt) REVERT: A 193 LYS cc_start: 0.7590 (mtpm) cc_final: 0.7180 (mmpt) REVERT: A 210 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7781 (mmtm) REVERT: A 277 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: A 309 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6863 (mt-10) REVERT: A 328 ASP cc_start: 0.7169 (m-30) cc_final: 0.6318 (m-30) REVERT: R 27 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7237 (mm) REVERT: R 72 ASN cc_start: 0.6625 (t0) cc_final: 0.6366 (t0) REVERT: R 127 ARG cc_start: 0.6928 (ptm160) cc_final: 0.6566 (ptt90) REVERT: R 187 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8142 (mt) REVERT: R 201 ARG cc_start: 0.7145 (ttp-170) cc_final: 0.6784 (ttm110) REVERT: R 368 ARG cc_start: 0.6301 (OUTLIER) cc_final: 0.5832 (ttt90) REVERT: H 87 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6990 (mtt90) REVERT: H 166 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8198 (tp) outliers start: 33 outliers final: 18 residues processed: 152 average time/residue: 1.3592 time to fit residues: 218.2612 Evaluate side-chains 151 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 368 ARG Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 181 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 86 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 100 optimal weight: 0.3980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8603 Z= 0.166 Angle : 0.548 10.337 11650 Z= 0.285 Chirality : 0.042 0.143 1328 Planarity : 0.004 0.044 1467 Dihedral : 4.549 40.001 1172 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.61 % Allowed : 16.87 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.85 (0.26), residues: 1049 helix: 2.44 (0.28), residues: 360 sheet: 0.38 (0.29), residues: 296 loop : -1.08 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.031 0.001 PHE R 369 TYR 0.012 0.001 TYR R 391 ARG 0.011 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8147 (tmmt) REVERT: A 24 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7754 (mtmt) REVERT: A 193 LYS cc_start: 0.7603 (mtpm) cc_final: 0.7181 (mmpt) REVERT: A 210 LYS cc_start: 0.8164 (ttmm) cc_final: 0.7795 (mmtm) REVERT: A 309 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6933 (mt-10) REVERT: A 328 ASP cc_start: 0.7157 (m-30) cc_final: 0.6309 (m-30) REVERT: R 27 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7260 (mm) REVERT: R 72 ASN cc_start: 0.6628 (t0) cc_final: 0.6371 (t0) REVERT: R 127 ARG cc_start: 0.7025 (ptm160) cc_final: 0.6627 (ptt90) REVERT: R 187 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8167 (mt) REVERT: R 201 ARG cc_start: 0.7151 (ttp-170) cc_final: 0.6790 (ttm110) REVERT: R 368 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5874 (ttt90) REVERT: H 87 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6988 (mtt90) REVERT: H 166 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8211 (tp) REVERT: H 212 VAL cc_start: 0.7398 (t) cc_final: 0.6995 (p) outliers start: 33 outliers final: 19 residues processed: 151 average time/residue: 1.3927 time to fit residues: 222.5041 Evaluate side-chains 152 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 368 ARG Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.0050 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 270 ASN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8603 Z= 0.218 Angle : 0.591 10.582 11650 Z= 0.308 Chirality : 0.043 0.153 1328 Planarity : 0.004 0.044 1467 Dihedral : 4.825 35.515 1172 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.72 % Allowed : 17.09 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.74 (0.26), residues: 1049 helix: 2.28 (0.27), residues: 361 sheet: 0.42 (0.29), residues: 291 loop : -1.16 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.032 0.002 PHE R 369 TYR 0.018 0.002 TYR H 59 ARG 0.011 0.001 ARG A 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8154 (tmmt) REVERT: A 24 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7776 (mtmt) REVERT: A 193 LYS cc_start: 0.7653 (mtpm) cc_final: 0.7205 (mmpt) REVERT: A 210 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7788 (mmtm) REVERT: A 277 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7044 (mm-30) REVERT: A 309 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7018 (mt-10) REVERT: A 328 ASP cc_start: 0.7168 (m-30) cc_final: 0.6255 (m-30) REVERT: R 27 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7331 (mm) REVERT: R 72 ASN cc_start: 0.6626 (t0) cc_final: 0.6370 (t0) REVERT: R 127 ARG cc_start: 0.7125 (ptm160) cc_final: 0.6672 (ptt90) REVERT: R 187 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8312 (mm) REVERT: R 201 ARG cc_start: 0.7170 (ttp-170) cc_final: 0.6803 (ttm110) REVERT: R 368 ARG cc_start: 0.6380 (OUTLIER) cc_final: 0.5944 (ttt90) REVERT: H 87 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6988 (mtt90) REVERT: H 166 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8253 (tp) outliers start: 34 outliers final: 19 residues processed: 154 average time/residue: 1.3672 time to fit residues: 222.1776 Evaluate side-chains 155 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 368 ARG Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 219 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 333 GLN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN H 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.162191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.151064 restraints weight = 8690.835| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 0.78 r_work: 0.3444 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8603 Z= 0.172 Angle : 0.562 10.853 11650 Z= 0.293 Chirality : 0.042 0.145 1328 Planarity : 0.004 0.045 1467 Dihedral : 4.658 37.787 1172 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.40 % Allowed : 17.96 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.86 (0.26), residues: 1049 helix: 2.36 (0.28), residues: 362 sheet: 0.42 (0.29), residues: 294 loop : -1.03 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.031 0.001 PHE R 369 TYR 0.012 0.001 TYR R 391 ARG 0.011 0.001 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4229.44 seconds wall clock time: 74 minutes 37.05 seconds (4477.05 seconds total)