Starting phenix.real_space_refine on Fri Jul 19 14:20:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/07_2024/8wca_37436_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/07_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_37436/07_2024/8wca_37436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/07_2024/8wca_37436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/07_2024/8wca_37436_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wca_37436/07_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-5388/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: 5.33, 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: 3.21 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: 0.98 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: 2.72 Time building geometry restraints manager: 3.50 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 2.440 nonbonded pdb=" OD1 ASN R 296 " pdb=" ND2 ASN R 300 " model vdw 2.188 2.520 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.218 2.440 nonbonded pdb=" OE2 GLU C 14 " pdb=" OG SER S 52 " model vdw 2.225 2.440 nonbonded pdb=" O SER R 198 " pdb=" OG SER R 198 " model vdw 2.243 2.440 ... (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 ========== 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.460 Find NCS groups from input model: 0.110 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.870 ------------------------------------------------------------------------------- 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 : 0.969 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: 0.2046 time to fit residues: 45.2340 Evaluate side-chains 121 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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: 0.9990 chunk 82 optimal weight: 0.0670 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN S 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1039 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= 0.188 Angle : 0.584 10.355 11386 Z= 0.303 Chirality : 0.044 0.143 1323 Planarity : 0.004 0.060 1443 Dihedral : 5.315 65.589 1194 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.03 % Allowed : 9.40 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1088 helix: 1.42 (0.28), residues: 374 sheet: 0.16 (0.35), residues: 265 loop : -1.23 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 291 HIS 0.004 0.001 HIS R 99 PHE 0.013 0.001 PHE C 223 TYR 0.014 0.001 TYR R 304 ARG 0.004 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 151 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 0.919 Fit side-chains REVERT: B 251 ARG cc_start: 0.7698 (mmt90) cc_final: 0.7425 (mmt-90) REVERT: C 22 GLN cc_start: 0.8571 (tp40) cc_final: 0.8290 (tp40) REVERT: C 345 ASP cc_start: 0.7447 (m-30) cc_final: 0.7125 (m-30) REVERT: R 218 LYS cc_start: 0.7182 (tppt) cc_final: 0.6436 (ttpt) outliers start: 16 outliers final: 14 residues processed: 140 average time/residue: 0.1876 time to fit residues: 36.9567 Evaluate side-chains 139 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 315 ILE 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 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: 4.9990 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8347 Z= 0.177 Angle : 0.538 9.456 11386 Z= 0.280 Chirality : 0.043 0.139 1323 Planarity : 0.004 0.047 1443 Dihedral : 4.710 54.815 1189 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.54 % Allowed : 12.07 % Favored : 85.39 % 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: 0.31 (0.26), residues: 1088 helix: 1.85 (0.28), residues: 373 sheet: 0.03 (0.34), residues: 270 loop : -1.10 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 291 HIS 0.004 0.001 HIS C 329 PHE 0.010 0.001 PHE C 223 TYR 0.014 0.001 TYR R 304 ARG 0.004 0.000 ARG C 314 *********************** 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 148 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.917 Fit side-chains REVERT: B 251 ARG cc_start: 0.7733 (mmt90) cc_final: 0.7481 (mmt-90) REVERT: C 345 ASP cc_start: 0.7330 (m-30) cc_final: 0.7006 (m-30) REVERT: C 359 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7760 (mt-10) outliers start: 20 outliers final: 13 residues processed: 137 average time/residue: 0.1940 time to fit residues: 36.4286 Evaluate side-chains 137 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 4 THR Chi-restraints excluded: chain C residue 181 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 66 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 94 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 8347 Z= 0.159 Angle : 0.529 13.271 11386 Z= 0.274 Chirality : 0.042 0.142 1323 Planarity : 0.003 0.034 1443 Dihedral : 4.143 47.520 1186 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.29 % Allowed : 13.85 % Favored : 83.86 % 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: 0.46 (0.27), residues: 1088 helix: 2.02 (0.28), residues: 375 sheet: 0.06 (0.33), residues: 281 loop : -1.07 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 291 HIS 0.003 0.001 HIS C 329 PHE 0.014 0.001 PHE R 185 TYR 0.011 0.001 TYR R 304 ARG 0.003 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 145 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 0.837 Fit side-chains REVERT: C 345 ASP cc_start: 0.7311 (m-30) cc_final: 0.7092 (m-30) REVERT: C 359 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: S 83 MET cc_start: 0.7249 (ptp) cc_final: 0.6998 (ptp) outliers start: 18 outliers final: 14 residues processed: 134 average time/residue: 0.1938 time to fit residues: 37.1151 Evaluate side-chains 135 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 4 THR Chi-restraints excluded: chain C residue 181 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 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 312 ARG 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: 1.9990 chunk 1 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8347 Z= 0.325 Angle : 0.618 10.598 11386 Z= 0.326 Chirality : 0.046 0.160 1323 Planarity : 0.004 0.033 1443 Dihedral : 4.414 37.495 1186 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.92 % Allowed : 14.74 % Favored : 82.34 % 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: 0.24 (0.26), residues: 1088 helix: 1.98 (0.27), residues: 367 sheet: 0.05 (0.35), residues: 266 loop : -1.32 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 148 HIS 0.007 0.002 HIS R 63 PHE 0.017 0.002 PHE R 268 TYR 0.019 0.002 TYR S 190 ARG 0.005 0.001 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 149 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.966 Fit side-chains REVERT: C 22 GLN cc_start: 0.8698 (tp40) cc_final: 0.8428 (tp40) REVERT: C 345 ASP cc_start: 0.7464 (m-30) cc_final: 0.7197 (m-30) REVERT: C 359 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7657 (mt-10) outliers start: 23 outliers final: 18 residues processed: 136 average time/residue: 0.1818 time to fit residues: 34.6663 Evaluate side-chains 141 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 4 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 292 THR 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 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 303 VAL 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: 0.8980 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 30.0000 chunk 101 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8347 Z= 0.339 Angle : 0.628 10.239 11386 Z= 0.332 Chirality : 0.046 0.152 1323 Planarity : 0.004 0.033 1443 Dihedral : 4.480 31.118 1186 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.56 % Allowed : 15.37 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1088 helix: 1.84 (0.27), residues: 366 sheet: -0.01 (0.34), residues: 266 loop : -1.43 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 310 HIS 0.007 0.002 HIS R 63 PHE 0.019 0.002 PHE R 268 TYR 0.018 0.002 TYR S 190 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 152 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 0.990 Fit side-chains REVERT: C 345 ASP cc_start: 0.7430 (m-30) cc_final: 0.7171 (m-30) REVERT: C 359 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7630 (mt-10) outliers start: 28 outliers final: 21 residues processed: 137 average time/residue: 0.1743 time to fit residues: 33.9503 Evaluate side-chains 138 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 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 B residue 142 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 181 THR 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 292 THR 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 126 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 303 VAL Chi-restraints excluded: chain S residue 184 SER 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: 0.8980 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 58 optimal weight: 0.0980 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8347 Z= 0.172 Angle : 0.553 9.795 11386 Z= 0.285 Chirality : 0.044 0.174 1323 Planarity : 0.003 0.033 1443 Dihedral : 4.077 24.140 1186 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.16 % Allowed : 17.15 % 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: 0.37 (0.27), residues: 1088 helix: 2.16 (0.28), residues: 366 sheet: -0.09 (0.34), residues: 280 loop : -1.18 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 310 HIS 0.003 0.001 HIS C 329 PHE 0.012 0.001 PHE R 185 TYR 0.012 0.001 TYR R 172 ARG 0.002 0.000 ARG C 314 *********************** 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 145 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.012 Fit side-chains REVERT: C 22 GLN cc_start: 0.8560 (tp40) cc_final: 0.8298 (tp40) REVERT: R 185 PHE cc_start: 0.6770 (t80) cc_final: 0.6564 (t80) outliers start: 17 outliers final: 14 residues processed: 138 average time/residue: 0.1717 time to fit residues: 33.5855 Evaluate side-chains 140 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 327 VAL Chi-restraints excluded: chain C residue 181 THR 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 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: 2.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 50.0000 chunk 100 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8347 Z= 0.294 Angle : 0.614 9.662 11386 Z= 0.321 Chirality : 0.046 0.181 1323 Planarity : 0.004 0.032 1443 Dihedral : 4.277 21.932 1186 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.41 % Allowed : 17.53 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1088 helix: 2.10 (0.28), residues: 364 sheet: 0.00 (0.34), residues: 265 loop : -1.34 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 310 HIS 0.007 0.001 HIS S 35 PHE 0.017 0.002 PHE R 268 TYR 0.018 0.002 TYR S 190 ARG 0.004 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 149 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 0.945 Fit side-chains REVERT: C 22 GLN cc_start: 0.8745 (tp40) cc_final: 0.8468 (tp40) REVERT: C 359 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7609 (mt-10) outliers start: 19 outliers final: 16 residues processed: 140 average time/residue: 0.1744 time to fit residues: 34.6770 Evaluate side-chains 136 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 142 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 181 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 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 R residue 303 VAL 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: 0.9980 chunk 100 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.0000 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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: 0.7236 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8347 Z= 0.178 Angle : 0.566 9.446 11386 Z= 0.293 Chirality : 0.044 0.206 1323 Planarity : 0.003 0.032 1443 Dihedral : 4.014 16.415 1186 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.29 % Allowed : 18.30 % Favored : 79.42 % 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: 0.41 (0.26), residues: 1088 helix: 2.19 (0.28), residues: 366 sheet: 0.04 (0.34), residues: 275 loop : -1.24 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 310 HIS 0.002 0.001 HIS B 91 PHE 0.017 0.001 PHE R 185 TYR 0.011 0.001 TYR C 285 ARG 0.005 0.000 ARG C 303 *********************** 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 143 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.849 Fit side-chains REVERT: C 22 GLN cc_start: 0.8597 (tp40) cc_final: 0.8363 (tp40) REVERT: C 359 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7589 (mt-10) outliers start: 18 outliers final: 15 residues processed: 133 average time/residue: 0.1724 time to fit residues: 32.6753 Evaluate side-chains 138 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 327 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 181 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8347 Z= 0.209 Angle : 0.583 10.383 11386 Z= 0.301 Chirality : 0.045 0.205 1323 Planarity : 0.003 0.040 1443 Dihedral : 4.011 16.182 1186 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.29 % Allowed : 18.42 % 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: 0.39 (0.26), residues: 1088 helix: 2.18 (0.27), residues: 366 sheet: -0.02 (0.33), residues: 277 loop : -1.20 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 291 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.001 PHE R 185 TYR 0.013 0.001 TYR S 190 ARG 0.003 0.000 ARG C 247 ********************** 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 143 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.933 Fit side-chains REVERT: C 22 GLN cc_start: 0.8645 (tp40) cc_final: 0.8413 (tp40) REVERT: C 359 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7574 (mt-10) outliers start: 18 outliers final: 16 residues processed: 134 average time/residue: 0.1749 time to fit residues: 33.2703 Evaluate side-chains 139 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 327 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 181 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.0470 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.202273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.165903 restraints weight = 9179.542| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.09 r_work: 0.3691 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8347 Z= 0.181 Angle : 0.565 11.071 11386 Z= 0.289 Chirality : 0.044 0.207 1323 Planarity : 0.003 0.046 1443 Dihedral : 3.905 16.162 1186 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.16 % Allowed : 18.68 % Favored : 79.16 % 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 (0.26), residues: 1088 helix: 2.33 (0.27), residues: 365 sheet: 0.05 (0.33), residues: 275 loop : -1.23 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 310 HIS 0.003 0.001 HIS B 91 PHE 0.018 0.001 PHE R 185 TYR 0.013 0.001 TYR C 285 ARG 0.003 0.000 ARG C 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1961.61 seconds wall clock time: 35 minutes 36.48 seconds (2136.48 seconds total)