Starting phenix.real_space_refine on Tue Sep 24 20:32:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ij3_35463/09_2024/8ij3_35463.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ij3_35463/09_2024/8ij3_35463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ij3_35463/09_2024/8ij3_35463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ij3_35463/09_2024/8ij3_35463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ij3_35463/09_2024/8ij3_35463.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ij3_35463/09_2024/8ij3_35463.cif" } resolution = 3.28 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= 0.018 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 66 5.16 5 C 5572 2.51 5 N 1507 2.21 5 O 1627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 8772 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2253 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 10, 'TRANS': 281} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1701 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 30 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Time building chain proxies: 5.96, per 1000 atoms: 0.68 Number of scatterers: 8772 At special positions: 0 Unit cell: (90.1, 120.7, 135.15, 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 66 16.00 O 1627 8.00 N 1507 7.00 C 5572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 2.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 35.5% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 removed outlier: 3.700A pdb=" N VAL A 27 " --> pdb=" O ASP A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 54 removed outlier: 3.875A pdb=" N VAL A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 removed outlier: 3.914A pdb=" N LEU A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 removed outlier: 3.666A pdb=" N LEU A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 131 Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.515A pdb=" N ASN A 137 " --> pdb=" O HIS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 160 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 191 through 218 removed outlier: 4.461A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 261 removed outlier: 3.576A pdb=" N LYS A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 270 through 284 removed outlier: 4.040A pdb=" N LEU A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 294 Proline residue: A 291 - end of helix removed outlier: 3.506A pdb=" N TYR A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.921A pdb=" N ILE C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 4.081A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.683A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 removed outlier: 3.738A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 329 No H-bonds generated for 'chain 'C' and resid 327 through 329' Processing helix chain 'C' and resid 330 through 352 Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.550A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.643A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.645A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.969A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.031A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.623A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.365A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.710A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 185 through 186 Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 186 removed outlier: 3.645A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.049A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.049A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.758A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 143 through 147 425 hydrogen bonds defined for protein. 1179 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: 2.73 Time building geometry restraints manager: 2.49 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: 2313 1.33 - 1.45: 1766 1.45 - 1.58: 4784 1.58 - 1.70: 0 1.70 - 1.82: 95 Bond restraints: 8958 Sorted by residual: bond pdb=" N VAL C 50 " pdb=" CA VAL C 50 " ideal model delta sigma weight residual 1.462 1.500 -0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" N GLY A 96 " pdb=" CA GLY A 96 " ideal model delta sigma weight residual 1.446 1.477 -0.031 9.70e-03 1.06e+04 1.04e+01 bond pdb=" N LYS C 51 " pdb=" CA LYS C 51 " ideal model delta sigma weight residual 1.458 1.499 -0.042 1.33e-02 5.65e+03 9.92e+00 bond pdb=" CA CYS C 351 " pdb=" C CYS C 351 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.36e-02 5.41e+03 9.10e+00 bond pdb=" CG HIS C 188 " pdb=" CD2 HIS C 188 " ideal model delta sigma weight residual 1.354 1.321 0.033 1.10e-02 8.26e+03 8.76e+00 ... (remaining 8953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.23: 12106 7.23 - 14.46: 24 14.46 - 21.70: 7 21.70 - 28.93: 4 28.93 - 36.16: 1 Bond angle restraints: 12142 Sorted by residual: angle pdb=" C PHE A 296 " pdb=" CA PHE A 296 " pdb=" CB PHE A 296 " ideal model delta sigma weight residual 111.23 75.07 36.16 1.63e+00 3.76e-01 4.92e+02 angle pdb=" N TYR C 290 " pdb=" CA TYR C 290 " pdb=" C TYR C 290 " ideal model delta sigma weight residual 108.31 135.54 -27.23 1.52e+00 4.33e-01 3.21e+02 angle pdb=" N PHE A 296 " pdb=" CA PHE A 296 " pdb=" C PHE A 296 " ideal model delta sigma weight residual 113.38 133.90 -20.52 1.17e+00 7.31e-01 3.08e+02 angle pdb=" N PHE A 244 " pdb=" CA PHE A 244 " pdb=" C PHE A 244 " ideal model delta sigma weight residual 113.18 127.57 -14.39 1.21e+00 6.83e-01 1.41e+02 angle pdb=" N HIS A 184 " pdb=" CA HIS A 184 " pdb=" C HIS A 184 " ideal model delta sigma weight residual 110.80 85.54 25.26 2.13e+00 2.20e-01 1.41e+02 ... (remaining 12137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4529 17.84 - 35.68: 574 35.68 - 53.52: 173 53.52 - 71.36: 23 71.36 - 89.20: 10 Dihedral angle restraints: 5309 sinusoidal: 2024 harmonic: 3285 Sorted by residual: dihedral pdb=" C PHE A 296 " pdb=" N PHE A 296 " pdb=" CA PHE A 296 " pdb=" CB PHE A 296 " ideal model delta harmonic sigma weight residual -122.60 -91.67 -30.93 0 2.50e+00 1.60e-01 1.53e+02 dihedral pdb=" C GLU C 289 " pdb=" N GLU C 289 " pdb=" CA GLU C 289 " pdb=" CB GLU C 289 " ideal model delta harmonic sigma weight residual -122.60 -150.67 28.07 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" N GLU C 289 " pdb=" C GLU C 289 " pdb=" CA GLU C 289 " pdb=" CB GLU C 289 " ideal model delta harmonic sigma weight residual 122.80 148.64 -25.84 0 2.50e+00 1.60e-01 1.07e+02 ... (remaining 5306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 1362 0.270 - 0.540: 10 0.540 - 0.811: 0 0.811 - 1.081: 0 1.081 - 1.351: 3 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CA GLU C 289 " pdb=" N GLU C 289 " pdb=" C GLU C 289 " pdb=" CB GLU C 289 " both_signs ideal model delta sigma weight residual False 2.51 1.16 1.35 2.00e-01 2.50e+01 4.56e+01 chirality pdb=" CA TYR C 290 " pdb=" N TYR C 290 " pdb=" C TYR C 290 " pdb=" CB TYR C 290 " both_signs ideal model delta sigma weight residual False 2.51 1.33 1.18 2.00e-01 2.50e+01 3.48e+01 chirality pdb=" CA PHE A 244 " pdb=" N PHE A 244 " pdb=" C PHE A 244 " pdb=" CB PHE A 244 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.09 2.00e-01 2.50e+01 2.94e+01 ... (remaining 1372 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 98 " 0.064 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO A 99 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.54e+00 pdb=" N PRO B 39 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 191 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C ALA A 191 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA A 191 " 0.015 2.00e-02 2.50e+03 pdb=" N MET A 192 " 0.013 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 177 2.67 - 3.22: 8004 3.22 - 3.78: 13155 3.78 - 4.34: 17210 4.34 - 4.90: 29914 Nonbonded interactions: 68460 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.107 3.040 nonbonded pdb=" NE2 HIS C 188 " pdb=" NE2 HIS C 195 " model vdw 2.127 3.200 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.190 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.221 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.224 3.040 ... (remaining 68455 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: 1.400 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.810 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 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 : 0.004 0.042 8958 Z= 0.251 Angle : 1.084 36.159 12142 Z= 0.656 Chirality : 0.079 1.351 1375 Planarity : 0.005 0.097 1546 Dihedral : 17.305 89.197 3170 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.71 % Allowed : 28.77 % Favored : 69.52 % Cbeta Deviations : 1.13 % Peptide Plane: Cis-proline : 3.23 % 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: -0.17 (0.26), residues: 1118 helix: 1.53 (0.28), residues: 372 sheet: -0.32 (0.30), residues: 276 loop : -1.31 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 93 HIS 0.005 0.001 HIS A 9 PHE 0.017 0.001 PHE A 95 TYR 0.023 0.001 TYR C 290 ARG 0.014 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.023 Fit side-chains REVERT: A 213 TRP cc_start: 0.8030 (t60) cc_final: 0.7519 (t-100) REVERT: B 175 GLN cc_start: 0.8145 (pp30) cc_final: 0.7932 (pp30) REVERT: C 350 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8040 (t0) outliers start: 16 outliers final: 5 residues processed: 147 average time/residue: 0.2566 time to fit residues: 49.5466 Evaluate side-chains 134 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 189 HIS S 130 GLN S 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8958 Z= 0.183 Angle : 0.552 9.480 12142 Z= 0.291 Chirality : 0.042 0.180 1375 Planarity : 0.004 0.053 1546 Dihedral : 5.200 56.201 1238 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.96 % Allowed : 26.42 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.23 (0.26), residues: 1118 helix: 2.08 (0.28), residues: 368 sheet: -0.28 (0.30), residues: 278 loop : -1.13 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS C 188 PHE 0.013 0.001 PHE A 277 TYR 0.017 0.001 TYR S 178 ARG 0.007 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 147 time to evaluate : 1.074 Fit side-chains REVERT: A 63 ARG cc_start: 0.8762 (mmt180) cc_final: 0.8465 (mmm-85) REVERT: A 84 MET cc_start: 0.7201 (ptp) cc_final: 0.6956 (ptp) REVERT: A 213 TRP cc_start: 0.7999 (t60) cc_final: 0.7523 (t-100) REVERT: A 288 MET cc_start: 0.7912 (ttp) cc_final: 0.7684 (ttp) REVERT: A 295 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.6222 (m-80) REVERT: B 215 GLU cc_start: 0.8473 (pp20) cc_final: 0.8258 (pp20) REVERT: B 234 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8769 (m-80) REVERT: B 258 ASP cc_start: 0.8234 (t0) cc_final: 0.8017 (t0) REVERT: B 268 ASN cc_start: 0.8385 (t0) cc_final: 0.8160 (t0) REVERT: B 338 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8626 (mm) outliers start: 37 outliers final: 16 residues processed: 171 average time/residue: 0.2350 time to fit residues: 53.5804 Evaluate side-chains 154 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 83 optimal weight: 0.1980 chunk 68 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 189 HIS A 223 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8958 Z= 0.233 Angle : 0.550 10.348 12142 Z= 0.289 Chirality : 0.042 0.140 1375 Planarity : 0.004 0.050 1546 Dihedral : 4.849 59.703 1227 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.28 % Allowed : 27.27 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.16 (0.26), residues: 1118 helix: 2.06 (0.27), residues: 373 sheet: -0.29 (0.30), residues: 280 loop : -1.27 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.011 0.001 HIS A 189 PHE 0.015 0.001 PHE C 189 TYR 0.016 0.001 TYR S 178 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 139 time to evaluate : 0.989 Fit side-chains REVERT: A 213 TRP cc_start: 0.8029 (t60) cc_final: 0.7507 (t-100) REVERT: A 285 MET cc_start: 0.8322 (mmm) cc_final: 0.7884 (tpt) REVERT: A 295 TYR cc_start: 0.6491 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: B 215 GLU cc_start: 0.8489 (pp20) cc_final: 0.8202 (pp20) REVERT: B 234 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8799 (m-80) REVERT: B 268 ASN cc_start: 0.8469 (t0) cc_final: 0.8178 (t0) REVERT: B 338 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8642 (mm) REVERT: G 21 MET cc_start: 0.7186 (tpp) cc_final: 0.6976 (tpp) REVERT: S 190 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8058 (ptt90) outliers start: 40 outliers final: 19 residues processed: 165 average time/residue: 0.2290 time to fit residues: 50.4478 Evaluate side-chains 161 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 207 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8958 Z= 0.195 Angle : 0.531 9.388 12142 Z= 0.279 Chirality : 0.041 0.132 1375 Planarity : 0.004 0.050 1546 Dihedral : 4.862 62.092 1227 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.81 % Allowed : 25.67 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.21 (0.26), residues: 1118 helix: 2.07 (0.27), residues: 379 sheet: -0.27 (0.30), residues: 280 loop : -1.25 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS A 9 PHE 0.014 0.001 PHE C 189 TYR 0.016 0.001 TYR S 178 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 145 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 213 TRP cc_start: 0.8027 (t60) cc_final: 0.7509 (t-100) REVERT: A 215 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8228 (mp) REVERT: A 232 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6672 (t80) REVERT: A 288 MET cc_start: 0.7994 (tmm) cc_final: 0.7710 (ttp) REVERT: A 295 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.6344 (m-80) REVERT: B 215 GLU cc_start: 0.8549 (pp20) cc_final: 0.8275 (pp20) REVERT: B 234 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8777 (m-80) REVERT: B 268 ASN cc_start: 0.8503 (t0) cc_final: 0.8166 (t0) REVERT: B 338 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8657 (mm) REVERT: G 21 MET cc_start: 0.7304 (tpp) cc_final: 0.7067 (tpp) REVERT: S 190 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7980 (ptt90) outliers start: 45 outliers final: 26 residues processed: 177 average time/residue: 0.2433 time to fit residues: 58.1643 Evaluate side-chains 170 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8958 Z= 0.209 Angle : 0.543 9.842 12142 Z= 0.284 Chirality : 0.042 0.198 1375 Planarity : 0.004 0.049 1546 Dihedral : 4.885 63.765 1227 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.13 % Allowed : 25.24 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.30 (0.26), residues: 1118 helix: 2.19 (0.27), residues: 373 sheet: -0.28 (0.30), residues: 291 loop : -1.17 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.007 0.001 HIS A 9 PHE 0.014 0.001 PHE A 277 TYR 0.016 0.001 TYR S 178 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 141 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.7432 (ptp) cc_final: 0.7227 (ptp) REVERT: A 213 TRP cc_start: 0.8045 (t60) cc_final: 0.7502 (t-100) REVERT: A 215 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8234 (mp) REVERT: A 232 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6626 (t80) REVERT: A 238 ILE cc_start: 0.7916 (mm) cc_final: 0.7624 (mm) REVERT: A 288 MET cc_start: 0.8092 (tmm) cc_final: 0.7784 (ttp) REVERT: A 295 TYR cc_start: 0.6442 (OUTLIER) cc_final: 0.6229 (m-80) REVERT: B 215 GLU cc_start: 0.8551 (pp20) cc_final: 0.8261 (pp20) REVERT: B 234 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8767 (m-80) REVERT: B 268 ASN cc_start: 0.8491 (t0) cc_final: 0.8160 (t0) REVERT: B 338 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8652 (mm) REVERT: C 283 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7769 (tt) REVERT: C 315 ASP cc_start: 0.8291 (p0) cc_final: 0.8055 (p0) REVERT: G 21 MET cc_start: 0.7388 (tpp) cc_final: 0.7095 (tpp) REVERT: S 190 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7969 (ptt90) outliers start: 48 outliers final: 30 residues processed: 174 average time/residue: 0.2308 time to fit residues: 53.7289 Evaluate side-chains 176 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 8958 Z= 0.411 Angle : 0.632 12.305 12142 Z= 0.335 Chirality : 0.045 0.143 1375 Planarity : 0.004 0.050 1546 Dihedral : 5.317 64.692 1227 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.35 % Allowed : 24.60 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.05 (0.25), residues: 1118 helix: 1.84 (0.27), residues: 379 sheet: -0.35 (0.30), residues: 279 loop : -1.44 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 47 HIS 0.006 0.001 HIS A 9 PHE 0.019 0.002 PHE B 199 TYR 0.018 0.002 TYR S 178 ARG 0.005 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 140 time to evaluate : 1.026 Fit side-chains REVERT: A 215 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8363 (mp) REVERT: A 232 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6624 (t80) REVERT: A 273 ASP cc_start: 0.8137 (t0) cc_final: 0.7099 (p0) REVERT: A 285 MET cc_start: 0.8471 (mmm) cc_final: 0.8066 (tpt) REVERT: A 288 MET cc_start: 0.8174 (tmm) cc_final: 0.7532 (tmm) REVERT: B 215 GLU cc_start: 0.8578 (pp20) cc_final: 0.8145 (pp20) REVERT: B 234 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8857 (m-80) REVERT: B 268 ASN cc_start: 0.8549 (t0) cc_final: 0.8287 (t0) REVERT: B 338 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8756 (mm) REVERT: C 283 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7781 (tt) REVERT: C 315 ASP cc_start: 0.8326 (p0) cc_final: 0.8060 (p0) REVERT: G 21 MET cc_start: 0.7409 (tpp) cc_final: 0.7092 (tpp) REVERT: S 190 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8050 (ptt90) REVERT: S 203 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8787 (p) outliers start: 50 outliers final: 30 residues processed: 173 average time/residue: 0.2340 time to fit residues: 53.9544 Evaluate side-chains 173 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.0000 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8958 Z= 0.164 Angle : 0.545 11.906 12142 Z= 0.283 Chirality : 0.041 0.171 1375 Planarity : 0.004 0.046 1546 Dihedral : 4.949 65.835 1227 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.39 % Allowed : 25.78 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.26 (0.26), residues: 1118 helix: 2.23 (0.28), residues: 368 sheet: -0.31 (0.30), residues: 286 loop : -1.20 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.005 0.001 HIS A 9 PHE 0.014 0.001 PHE A 277 TYR 0.015 0.001 TYR S 178 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 145 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8739 (mm) cc_final: 0.8514 (mm) REVERT: A 213 TRP cc_start: 0.8006 (t60) cc_final: 0.7535 (t-100) REVERT: A 215 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8264 (mp) REVERT: A 232 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6519 (t80) REVERT: A 273 ASP cc_start: 0.8036 (t0) cc_final: 0.7077 (p0) REVERT: A 285 MET cc_start: 0.8322 (mmm) cc_final: 0.7801 (tpt) REVERT: A 288 MET cc_start: 0.8100 (tmm) cc_final: 0.7459 (tmm) REVERT: B 215 GLU cc_start: 0.8619 (pp20) cc_final: 0.8326 (pp20) REVERT: B 234 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8750 (m-80) REVERT: B 268 ASN cc_start: 0.8537 (t0) cc_final: 0.8256 (t0) REVERT: B 338 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8637 (mm) REVERT: C 283 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7797 (tt) REVERT: C 315 ASP cc_start: 0.8263 (p0) cc_final: 0.8012 (p0) REVERT: G 21 MET cc_start: 0.7574 (tpp) cc_final: 0.7200 (tpp) REVERT: S 190 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7822 (ptt90) outliers start: 41 outliers final: 26 residues processed: 174 average time/residue: 0.2322 time to fit residues: 53.8478 Evaluate side-chains 172 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8958 Z= 0.263 Angle : 0.582 12.916 12142 Z= 0.304 Chirality : 0.042 0.154 1375 Planarity : 0.004 0.046 1546 Dihedral : 5.038 65.533 1227 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 3.96 % Allowed : 25.99 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.28 (0.26), residues: 1118 helix: 2.21 (0.27), residues: 368 sheet: -0.27 (0.30), residues: 285 loop : -1.19 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 9 PHE 0.015 0.002 PHE A 277 TYR 0.016 0.001 TYR S 178 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8747 (mm) cc_final: 0.8516 (mm) REVERT: A 215 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8289 (mp) REVERT: A 232 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6555 (t80) REVERT: A 273 ASP cc_start: 0.8065 (t0) cc_final: 0.7056 (p0) REVERT: B 215 GLU cc_start: 0.8605 (pp20) cc_final: 0.8303 (pp20) REVERT: B 234 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8826 (m-80) REVERT: B 268 ASN cc_start: 0.8596 (t0) cc_final: 0.8298 (t0) REVERT: B 338 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8672 (mm) REVERT: C 283 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7805 (tt) REVERT: C 315 ASP cc_start: 0.8258 (p0) cc_final: 0.8052 (p0) REVERT: G 21 MET cc_start: 0.7570 (tpp) cc_final: 0.7197 (tpp) REVERT: S 76 LYS cc_start: 0.8310 (mtmm) cc_final: 0.7925 (pttp) REVERT: S 190 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7836 (ptt90) outliers start: 37 outliers final: 27 residues processed: 167 average time/residue: 0.2347 time to fit residues: 52.7300 Evaluate side-chains 169 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8958 Z= 0.229 Angle : 0.577 13.286 12142 Z= 0.300 Chirality : 0.042 0.157 1375 Planarity : 0.004 0.046 1546 Dihedral : 5.016 65.814 1227 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.29 % Favored : 95.62 % Rotamer: Outliers : 4.28 % Allowed : 25.56 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.28 (0.26), residues: 1118 helix: 2.20 (0.27), residues: 368 sheet: -0.27 (0.30), residues: 285 loop : -1.17 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.005 0.001 HIS A 9 PHE 0.014 0.001 PHE A 277 TYR 0.015 0.001 TYR S 178 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 137 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8744 (mm) cc_final: 0.8530 (mm) REVERT: A 213 TRP cc_start: 0.8050 (t60) cc_final: 0.7534 (t-100) REVERT: A 215 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8276 (mp) REVERT: A 232 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6531 (t80) REVERT: A 273 ASP cc_start: 0.8043 (t0) cc_final: 0.7055 (p0) REVERT: B 215 GLU cc_start: 0.8624 (pp20) cc_final: 0.8327 (pp20) REVERT: B 234 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8828 (m-80) REVERT: B 268 ASN cc_start: 0.8590 (t0) cc_final: 0.8286 (t0) REVERT: B 338 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8655 (mm) REVERT: C 283 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7827 (tt) REVERT: C 315 ASP cc_start: 0.8272 (p0) cc_final: 0.8056 (p0) REVERT: G 21 MET cc_start: 0.7593 (tpp) cc_final: 0.7196 (tpp) REVERT: S 76 LYS cc_start: 0.8356 (mtmm) cc_final: 0.7937 (pttp) REVERT: S 190 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7831 (ptt90) outliers start: 40 outliers final: 30 residues processed: 168 average time/residue: 0.2345 time to fit residues: 52.8693 Evaluate side-chains 171 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 135 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8958 Z= 0.213 Angle : 0.594 13.496 12142 Z= 0.305 Chirality : 0.041 0.151 1375 Planarity : 0.004 0.046 1546 Dihedral : 5.004 66.103 1227 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.17 % Rotamer: Outliers : 4.17 % Allowed : 26.10 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.31 (0.26), residues: 1118 helix: 2.19 (0.27), residues: 368 sheet: -0.24 (0.30), residues: 285 loop : -1.13 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 93 HIS 0.005 0.001 HIS A 9 PHE 0.014 0.001 PHE A 277 TYR 0.019 0.001 TYR C 302 ARG 0.006 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8757 (mm) cc_final: 0.8526 (mm) REVERT: A 213 TRP cc_start: 0.8043 (t60) cc_final: 0.7545 (t-100) REVERT: A 215 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8212 (mp) REVERT: A 232 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6534 (t80) REVERT: A 273 ASP cc_start: 0.8073 (t0) cc_final: 0.7063 (p0) REVERT: B 175 GLN cc_start: 0.8040 (pp30) cc_final: 0.7840 (pp30) REVERT: B 215 GLU cc_start: 0.8632 (pp20) cc_final: 0.8338 (pp20) REVERT: B 234 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8830 (m-80) REVERT: B 268 ASN cc_start: 0.8563 (t0) cc_final: 0.8265 (t0) REVERT: B 338 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8643 (mm) REVERT: C 283 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7812 (tt) REVERT: C 315 ASP cc_start: 0.8273 (p0) cc_final: 0.8045 (p0) REVERT: G 21 MET cc_start: 0.7625 (tpp) cc_final: 0.7227 (tpp) REVERT: S 76 LYS cc_start: 0.8345 (mtmm) cc_final: 0.7926 (pttp) REVERT: S 190 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7864 (ptt90) outliers start: 39 outliers final: 31 residues processed: 165 average time/residue: 0.2374 time to fit residues: 52.9707 Evaluate side-chains 172 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 135 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 77 optimal weight: 0.0570 chunk 5 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.106012 restraints weight = 11388.809| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.51 r_work: 0.2985 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8958 Z= 0.257 Angle : 0.610 13.504 12142 Z= 0.313 Chirality : 0.042 0.147 1375 Planarity : 0.004 0.046 1546 Dihedral : 5.061 66.013 1227 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 4.17 % Allowed : 26.20 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.22 (0.26), residues: 1118 helix: 2.05 (0.27), residues: 374 sheet: -0.25 (0.30), residues: 286 loop : -1.20 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 93 HIS 0.004 0.001 HIS A 9 PHE 0.014 0.001 PHE A 277 TYR 0.016 0.001 TYR S 178 ARG 0.006 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2172.82 seconds wall clock time: 39 minutes 13.63 seconds (2353.63 seconds total)