Starting phenix.real_space_refine on Sat Aug 3 13:10:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/08_2024/8wca_37436_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/08_2024/8wca_37436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/08_2024/8wca_37436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/08_2024/8wca_37436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/08_2024/8wca_37436_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/08_2024/8wca_37436_neut.cif" } resolution = 3.48 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= -0.002 sd= 0.078 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 5232 2.51 5 N 1374 2.21 5 O 1499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 215": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "R PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 42": "OE1" <-> "OE2" Residue "Y GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8160 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2336 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 5, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 11, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 127 Chain: "C" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1799 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2010 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 229 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'HIS:plan': 6, 'TYR:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 97 Chain: "S" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1666 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "Y" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 340 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'PEA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.34, per 1000 atoms: 0.65 Number of scatterers: 8160 At special positions: 0 Unit cell: (103.96, 117.76, 124.2, 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 1499 8.00 N 1374 7.00 C 5232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 37.3% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'B' and resid 13 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 6 through 20 removed outlier: 3.692A pdb=" N LYS C 10 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 32 removed outlier: 3.511A pdb=" N ASP C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 32 " --> pdb=" O GLN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 54 removed outlier: 3.536A pdb=" N ARG C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.715A pdb=" N ASN C 216 " --> pdb=" O GLN C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 274 through 279 Processing helix chain 'C' and resid 280 through 283 removed outlier: 4.036A pdb=" N ALA C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 298 through 319 removed outlier: 4.062A pdb=" N ILE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER C 319 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 358 Processing helix chain 'R' and resid 23 through 47 Processing helix chain 'R' and resid 59 through 85 removed outlier: 3.734A pdb=" N HIS R 63 " --> pdb=" O ASN R 59 " (cutoff:3.500A) Proline residue: R 78 - end of helix removed outlier: 4.496A pdb=" N ALA R 85 " --> pdb=" O MET R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 125 removed outlier: 4.267A pdb=" N SER R 107 " --> pdb=" O ASP R 103 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER R 108 " --> pdb=" O ILE R 104 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL R 125 " --> pdb=" O ARG R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 129 No H-bonds generated for 'chain 'R' and resid 127 through 129' Processing helix chain 'R' and resid 130 through 135 removed outlier: 3.610A pdb=" N LYS R 134 " --> pdb=" O ARG R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 161 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 168 through 179 Processing helix chain 'R' and resid 187 through 199 removed outlier: 3.784A pdb=" N VAL R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU R 193 " --> pdb=" O ILE R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 224 removed outlier: 4.090A pdb=" N CYS R 208 " --> pdb=" O SER R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 277 removed outlier: 3.889A pdb=" N THR R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU R 253 " --> pdb=" O ALA R 249 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 307 removed outlier: 3.727A pdb=" N ASN R 286 " --> pdb=" O PRO R 282 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL R 288 " --> pdb=" O THR R 284 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR R 298 " --> pdb=" O TYR R 294 " (cutoff:3.500A) Proline residue: R 301 - end of helix removed outlier: 3.555A pdb=" N PHE R 307 " --> pdb=" O VAL R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 319 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.649A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.920A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 25 removed outlier: 3.890A pdb=" N ILE Y 25 " --> pdb=" O MET Y 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 45 removed outlier: 3.923A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA Y 34 " --> pdb=" O VAL Y 30 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.956A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.902A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.384A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.107A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 229 through 234 Processing sheet with id=AA6, first strand: chain 'B' and resid 276 through 277 removed outlier: 6.798A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 315 through 317 removed outlier: 6.893A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 184 through 185 Processing sheet with id=AA9, first strand: chain 'C' and resid 184 through 185 removed outlier: 4.332A pdb=" N VAL C 201 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA C 220 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 225 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL C 254 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.684A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 11 removed outlier: 5.957A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'S' and resid 45 through 51 removed outlier: 6.689A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.692A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.719A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1113 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: 2.18 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1300 1.27 - 1.41: 2226 1.41 - 1.54: 4705 1.54 - 1.68: 35 1.68 - 1.81: 81 Bond restraints: 8347 Sorted by residual: bond pdb=" C ASN R 41 " pdb=" O ASN R 41 " ideal model delta sigma weight residual 1.236 1.138 0.099 1.26e-02 6.30e+03 6.13e+01 bond pdb=" C ARG C 356 " pdb=" O ARG C 356 " ideal model delta sigma weight residual 1.236 1.143 0.093 1.31e-02 5.83e+03 5.06e+01 bond pdb=" CA ARG C 356 " pdb=" C ARG C 356 " ideal model delta sigma weight residual 1.520 1.423 0.097 1.39e-02 5.18e+03 4.91e+01 bond pdb=" CA ASN R 41 " pdb=" C ASN R 41 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.35e-02 5.49e+03 3.92e+01 bond pdb=" C ARG B 49 " pdb=" O ARG B 49 " ideal model delta sigma weight residual 1.235 1.175 0.060 1.00e-02 1.00e+04 3.55e+01 ... (remaining 8342 not shown) Histogram of bond angle deviations from ideal: 98.39 - 106.01: 165 106.01 - 113.64: 4563 113.64 - 121.26: 4384 121.26 - 128.88: 2206 128.88 - 136.51: 68 Bond angle restraints: 11386 Sorted by residual: angle pdb=" N CYS R 96 " pdb=" CA CYS R 96 " pdb=" C CYS R 96 " ideal model delta sigma weight residual 113.43 101.23 12.20 1.26e+00 6.30e-01 9.37e+01 angle pdb=" N GLY R 92 " pdb=" CA GLY R 92 " pdb=" C GLY R 92 " ideal model delta sigma weight residual 111.93 122.92 -10.99 1.15e+00 7.56e-01 9.13e+01 angle pdb=" N LEU B 55 " pdb=" CA LEU B 55 " pdb=" C LEU B 55 " ideal model delta sigma weight residual 111.07 118.67 -7.60 1.07e+00 8.73e-01 5.04e+01 angle pdb=" N ARG C 356 " pdb=" CA ARG C 356 " pdb=" C ARG C 356 " ideal model delta sigma weight residual 114.31 105.32 8.99 1.29e+00 6.01e-01 4.85e+01 angle pdb=" N VAL R 192 " pdb=" CA VAL R 192 " pdb=" C VAL R 192 " ideal model delta sigma weight residual 110.42 103.94 6.48 9.60e-01 1.09e+00 4.56e+01 ... (remaining 11381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4452 17.98 - 35.97: 305 35.97 - 53.95: 64 53.95 - 71.93: 6 71.93 - 89.92: 6 Dihedral angle restraints: 4833 sinusoidal: 1604 harmonic: 3229 Sorted by residual: dihedral pdb=" N LEU R 193 " pdb=" C LEU R 193 " pdb=" CA LEU R 193 " pdb=" CB LEU R 193 " ideal model delta harmonic sigma weight residual 122.80 134.87 -12.07 0 2.50e+00 1.60e-01 2.33e+01 dihedral pdb=" C ARG B 49 " pdb=" N ARG B 49 " pdb=" CA ARG B 49 " pdb=" CB ARG B 49 " ideal model delta harmonic sigma weight residual -122.60 -110.73 -11.87 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" C TYR R 90 " pdb=" N TYR R 90 " pdb=" CA TYR R 90 " pdb=" CB TYR R 90 " ideal model delta harmonic sigma weight residual -122.60 -111.10 -11.50 0 2.50e+00 1.60e-01 2.12e+01 ... (remaining 4830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1272 0.120 - 0.240: 40 0.240 - 0.361: 6 0.361 - 0.481: 2 0.481 - 0.601: 3 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA LEU R 193 " pdb=" N LEU R 193 " pdb=" C LEU R 193 " pdb=" CB LEU R 193 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.03e+00 chirality pdb=" CA ASN R 41 " pdb=" N ASN R 41 " pdb=" C ASN R 41 " pdb=" CB ASN R 41 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" CA SER R 198 " pdb=" N SER R 198 " pdb=" C SER R 198 " pdb=" CB SER R 198 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.46e+00 ... (remaining 1320 not shown) Planarity restraints: 1443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 35 " -0.024 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C LEU R 35 " 0.083 2.00e-02 2.50e+03 pdb=" O LEU R 35 " -0.032 2.00e-02 2.50e+03 pdb=" N THR R 36 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 355 " -0.024 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C LEU C 355 " 0.083 2.00e-02 2.50e+03 pdb=" O LEU C 355 " -0.029 2.00e-02 2.50e+03 pdb=" N ARG C 356 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 96 " 0.022 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C CYS R 96 " -0.074 2.00e-02 2.50e+03 pdb=" O CYS R 96 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS R 97 " 0.025 2.00e-02 2.50e+03 ... (remaining 1440 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 158 2.66 - 3.22: 7534 3.22 - 3.78: 11823 3.78 - 4.34: 15482 4.34 - 4.90: 26720 Nonbonded interactions: 61717 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.105 3.040 nonbonded pdb=" OD1 ASN R 296 " pdb=" ND2 ASN R 300 " model vdw 2.188 3.120 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.218 3.040 nonbonded pdb=" OE2 GLU C 14 " pdb=" OG SER S 52 " model vdw 2.225 3.040 nonbonded pdb=" O SER R 198 " pdb=" OG SER R 198 " model vdw 2.243 3.040 ... (remaining 61712 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: 1.230 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.550 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 : 0.006 0.099 8347 Z= 0.451 Angle : 0.875 12.199 11386 Z= 0.542 Chirality : 0.063 0.601 1323 Planarity : 0.006 0.090 1443 Dihedral : 13.523 89.915 2741 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.89 % Allowed : 0.89 % Favored : 98.22 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 1088 helix: 0.83 (0.29), residues: 372 sheet: 0.07 (0.34), residues: 267 loop : -1.39 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 291 HIS 0.006 0.001 HIS B 225 PHE 0.044 0.002 PHE R 154 TYR 0.017 0.001 TYR R 90 ARG 0.010 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 0.980 Fit side-chains REVERT: B 251 ARG cc_start: 0.7651 (mmt90) cc_final: 0.7358 (mmt-90) REVERT: C 22 GLN cc_start: 0.8398 (tp40) cc_final: 0.7978 (tp40) REVERT: C 345 ASP cc_start: 0.7465 (m-30) cc_final: 0.7260 (m-30) REVERT: S 5 VAL cc_start: 0.7306 (t) cc_final: 0.7046 (p) outliers start: 7 outliers final: 5 residues processed: 160 average time/residue: 0.1807 time to fit residues: 39.8255 Evaluate side-chains 121 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 89 TRP Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 154 PHE Chi-restraints excluded: chain R residue 185 PHE Chi-restraints excluded: chain R residue 194 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0670 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 ASN C 259 ASN S 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8347 Z= 0.249 Angle : 0.626 10.923 11386 Z= 0.328 Chirality : 0.046 0.148 1323 Planarity : 0.004 0.061 1443 Dihedral : 5.485 63.511 1194 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.16 % Allowed : 10.04 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1088 helix: 1.28 (0.27), residues: 373 sheet: 0.03 (0.34), residues: 269 loop : -1.25 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 291 HIS 0.005 0.001 HIS S 35 PHE 0.013 0.002 PHE R 268 TYR 0.015 0.001 TYR S 190 ARG 0.005 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 0.962 Fit side-chains REVERT: B 251 ARG cc_start: 0.7709 (mmt90) cc_final: 0.7443 (mmt-90) REVERT: C 22 GLN cc_start: 0.8657 (tp40) cc_final: 0.8333 (tp40) REVERT: C 345 ASP cc_start: 0.7442 (m-30) cc_final: 0.7095 (m-30) REVERT: C 359 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: S 113 GLN cc_start: 0.8592 (tp40) cc_final: 0.8320 (mm-40) outliers start: 17 outliers final: 15 residues processed: 140 average time/residue: 0.1932 time to fit residues: 38.6816 Evaluate side-chains 142 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain R residue 89 TRP Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 30.0000 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8347 Z= 0.296 Angle : 0.623 10.883 11386 Z= 0.329 Chirality : 0.046 0.146 1323 Planarity : 0.004 0.046 1443 Dihedral : 5.152 53.033 1189 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.54 % Allowed : 14.10 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1088 helix: 1.59 (0.27), residues: 370 sheet: -0.14 (0.34), residues: 277 loop : -1.35 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 291 HIS 0.006 0.002 HIS S 35 PHE 0.016 0.002 PHE R 268 TYR 0.016 0.002 TYR S 190 ARG 0.004 0.000 ARG C 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.821 Fit side-chains REVERT: C 22 GLN cc_start: 0.8716 (tp40) cc_final: 0.8398 (tp40) REVERT: C 345 ASP cc_start: 0.7454 (m-30) cc_final: 0.7091 (m-30) REVERT: C 359 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: S 113 GLN cc_start: 0.8622 (tp40) cc_final: 0.8383 (mm-40) outliers start: 20 outliers final: 17 residues processed: 136 average time/residue: 0.1798 time to fit residues: 34.6908 Evaluate side-chains 142 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain R residue 89 TRP Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 0.0570 chunk 66 optimal weight: 0.1980 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN C 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8347 Z= 0.180 Angle : 0.563 9.983 11386 Z= 0.293 Chirality : 0.044 0.154 1323 Planarity : 0.004 0.034 1443 Dihedral : 4.700 47.277 1189 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.54 % Allowed : 15.50 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1088 helix: 1.93 (0.27), residues: 370 sheet: -0.10 (0.34), residues: 284 loop : -1.24 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 291 HIS 0.003 0.001 HIS C 329 PHE 0.011 0.001 PHE R 268 TYR 0.012 0.001 TYR R 304 ARG 0.004 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 0.991 Fit side-chains REVERT: C 22 GLN cc_start: 0.8578 (tp40) cc_final: 0.8331 (tp40) REVERT: C 53 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6329 (mpt) REVERT: C 359 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: R 193 LEU cc_start: 0.7974 (tt) cc_final: 0.7716 (mt) REVERT: S 113 GLN cc_start: 0.8601 (tp40) cc_final: 0.8354 (mm-40) REVERT: S 140 MET cc_start: 0.7646 (mmm) cc_final: 0.6913 (mmm) outliers start: 20 outliers final: 13 residues processed: 138 average time/residue: 0.1741 time to fit residues: 34.0868 Evaluate side-chains 138 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 184 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.0670 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- 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: 0.7276 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8347 Z= 0.235 Angle : 0.577 9.495 11386 Z= 0.304 Chirality : 0.045 0.149 1323 Planarity : 0.004 0.035 1443 Dihedral : 4.271 33.576 1186 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.67 % Allowed : 16.65 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1088 helix: 1.98 (0.27), residues: 368 sheet: -0.06 (0.34), residues: 271 loop : -1.31 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 310 HIS 0.005 0.001 HIS S 35 PHE 0.014 0.001 PHE R 268 TYR 0.015 0.001 TYR C 30 ARG 0.003 0.000 ARG C 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 0.897 Fit side-chains REVERT: C 22 GLN cc_start: 0.8649 (tp40) cc_final: 0.8382 (tp40) REVERT: C 53 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6538 (mpt) REVERT: C 359 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7766 (mt-10) outliers start: 21 outliers final: 14 residues processed: 134 average time/residue: 0.1789 time to fit residues: 33.9303 Evaluate side-chains 136 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 30.0000 chunk 101 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8347 Z= 0.284 Angle : 0.604 10.041 11386 Z= 0.319 Chirality : 0.046 0.153 1323 Planarity : 0.004 0.033 1443 Dihedral : 4.352 27.807 1186 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.80 % Allowed : 17.92 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.15 (0.26), residues: 1088 helix: 1.92 (0.27), residues: 368 sheet: -0.06 (0.34), residues: 269 loop : -1.36 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 310 HIS 0.006 0.001 HIS S 35 PHE 0.018 0.002 PHE R 268 TYR 0.018 0.002 TYR B 105 ARG 0.004 0.000 ARG C 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 0.999 Fit side-chains REVERT: C 22 GLN cc_start: 0.8693 (tp40) cc_final: 0.8389 (tp40) REVERT: C 53 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6578 (mpt) REVERT: C 359 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: S 140 MET cc_start: 0.7810 (mmm) cc_final: 0.7044 (mmm) outliers start: 22 outliers final: 17 residues processed: 135 average time/residue: 0.1903 time to fit residues: 36.1713 Evaluate side-chains 141 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 41 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8347 Z= 0.173 Angle : 0.548 8.395 11386 Z= 0.288 Chirality : 0.044 0.174 1323 Planarity : 0.003 0.034 1443 Dihedral : 4.066 21.085 1186 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.80 % Allowed : 18.17 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 1088 helix: 2.14 (0.28), residues: 368 sheet: -0.07 (0.34), residues: 281 loop : -1.23 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 291 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE R 165 TYR 0.015 0.001 TYR R 172 ARG 0.006 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: C 22 GLN cc_start: 0.8552 (tp40) cc_final: 0.8324 (tp40) REVERT: C 53 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6628 (mpt) REVERT: C 359 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7633 (mt-10) REVERT: R 193 LEU cc_start: 0.7888 (tt) cc_final: 0.7561 (mt) REVERT: S 140 MET cc_start: 0.7804 (mmm) cc_final: 0.6961 (mmm) outliers start: 22 outliers final: 16 residues processed: 138 average time/residue: 0.1802 time to fit residues: 34.8572 Evaluate side-chains 143 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN R 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8347 Z= 0.259 Angle : 0.592 9.200 11386 Z= 0.312 Chirality : 0.046 0.194 1323 Planarity : 0.004 0.034 1443 Dihedral : 4.164 18.430 1186 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.92 % Allowed : 18.93 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1088 helix: 2.11 (0.27), residues: 367 sheet: -0.13 (0.34), residues: 274 loop : -1.33 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 310 HIS 0.006 0.001 HIS S 35 PHE 0.014 0.002 PHE R 268 TYR 0.017 0.002 TYR B 105 ARG 0.003 0.000 ARG C 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 0.959 Fit side-chains REVERT: C 22 GLN cc_start: 0.8632 (tp40) cc_final: 0.8384 (tp40) REVERT: C 53 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6628 (mpt) REVERT: C 359 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7599 (mt-10) outliers start: 23 outliers final: 16 residues processed: 132 average time/residue: 0.1840 time to fit residues: 34.0144 Evaluate side-chains 134 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.0980 chunk 100 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 8347 Z= 0.164 Angle : 0.546 7.595 11386 Z= 0.285 Chirality : 0.044 0.202 1323 Planarity : 0.003 0.033 1443 Dihedral : 3.916 16.376 1186 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.03 % Allowed : 19.82 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.27), residues: 1088 helix: 2.36 (0.27), residues: 363 sheet: -0.09 (0.35), residues: 263 loop : -1.11 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 310 HIS 0.002 0.001 HIS B 91 PHE 0.011 0.001 PHE C 189 TYR 0.011 0.001 TYR S 50 ARG 0.003 0.000 ARG C 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.308 Fit side-chains REVERT: C 53 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6640 (mpt) REVERT: C 359 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: R 257 MET cc_start: 0.7155 (mmt) cc_final: 0.6775 (mmm) REVERT: S 140 MET cc_start: 0.7777 (mmm) cc_final: 0.7144 (mmm) outliers start: 16 outliers final: 12 residues processed: 136 average time/residue: 0.1843 time to fit residues: 35.0379 Evaluate side-chains 134 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 108 optimal weight: 0.0020 chunk 99 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- 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: 0.7251 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8347 Z= 0.206 Angle : 0.573 8.452 11386 Z= 0.300 Chirality : 0.044 0.213 1323 Planarity : 0.003 0.033 1443 Dihedral : 3.954 16.207 1186 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.16 % Allowed : 20.20 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 1088 helix: 2.27 (0.27), residues: 368 sheet: 0.03 (0.34), residues: 276 loop : -1.19 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 310 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE R 268 TYR 0.013 0.001 TYR S 190 ARG 0.002 0.000 ARG C 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.882 Fit side-chains REVERT: B 251 ARG cc_start: 0.7656 (mmt90) cc_final: 0.7391 (mmt-90) REVERT: C 53 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6675 (mpt) REVERT: C 359 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7583 (mt-10) REVERT: S 140 MET cc_start: 0.7798 (mmm) cc_final: 0.7186 (mmm) outliers start: 17 outliers final: 15 residues processed: 133 average time/residue: 0.1952 time to fit residues: 35.9876 Evaluate side-chains 137 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 chunk 86 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.204563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.167623 restraints weight = 9144.603| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.04 r_work: 0.3724 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 8347 Z= 0.161 Angle : 0.553 8.104 11386 Z= 0.290 Chirality : 0.044 0.216 1323 Planarity : 0.003 0.034 1443 Dihedral : 3.842 16.493 1186 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.03 % Allowed : 20.84 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.27), residues: 1088 helix: 2.41 (0.27), residues: 364 sheet: 0.07 (0.34), residues: 277 loop : -1.04 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 310 HIS 0.002 0.001 HIS B 225 PHE 0.012 0.001 PHE C 189 TYR 0.011 0.001 TYR S 50 ARG 0.004 0.000 ARG C 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1955.29 seconds wall clock time: 35 minutes 38.84 seconds (2138.84 seconds total)