Starting phenix.real_space_refine on Tue Apr 29 00:08:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iod_35616/04_2025/8iod_35616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iod_35616/04_2025/8iod_35616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iod_35616/04_2025/8iod_35616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iod_35616/04_2025/8iod_35616.map" model { file = "/net/cci-nas-00/data/ceres_data/8iod_35616/04_2025/8iod_35616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iod_35616/04_2025/8iod_35616.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.051 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 67 5.16 5 C 5110 2.51 5 N 1401 2.21 5 O 1482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "L ASP 2": not complete - not flipped Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8061 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1943 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2567 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Chain: "G" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 405 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "L" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 74 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'4J2:plan-2': 1, 'NLE:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 946 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2124 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 5, 'TRANS': 264} Chain breaks: 1 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.67 Number of scatterers: 8061 At special positions: 0 Unit cell: (85.68, 93.177, 127.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 67 16.00 O 1482 8.00 N 1401 7.00 C 5110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 264 " - pdb=" SG CYS R 270 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.0 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 4J2 L 4 " Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 40.1% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.658A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.528A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.081A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.982A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 317 removed outlier: 3.524A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 removed outlier: 3.744A pdb=" N ILE A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.747A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.574A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.898A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 43 Processing helix chain 'R' and resid 44 through 60 removed outlier: 3.530A pdb=" N GLU R 53 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU R 56 " --> pdb=" O LEU R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 101 Processing helix chain 'R' and resid 107 through 146 Processing helix chain 'R' and resid 155 through 180 removed outlier: 4.399A pdb=" N ILE R 178 " --> pdb=" O GLY R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 220 removed outlier: 3.882A pdb=" N PHE R 194 " --> pdb=" O LEU R 190 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU R 200 " --> pdb=" O ALA R 196 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG R 218 " --> pdb=" O THR R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 247 removed outlier: 3.637A pdb=" N PHE R 247 " --> pdb=" O LEU R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 261 Processing helix chain 'R' and resid 267 through 275 removed outlier: 3.583A pdb=" N PHE R 273 " --> pdb=" O TYR R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 296 removed outlier: 3.990A pdb=" N SER R 288 " --> pdb=" O ILE R 284 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL R 289 " --> pdb=" O MET R 285 " (cutoff:3.500A) Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 312 removed outlier: 3.627A pdb=" N CYS R 312 " --> pdb=" O GLU R 308 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 189 removed outlier: 6.226A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.314A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.390A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.089A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.226A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.838A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.763A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.552A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.776A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.904A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1152 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: 2.39 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2029 1.33 - 1.45: 1651 1.45 - 1.57: 4443 1.57 - 1.69: 0 1.69 - 1.82: 99 Bond restraints: 8222 Sorted by residual: bond pdb=" CG ASP L 2 " pdb=" OD1 ASP L 2 " ideal model delta sigma weight residual 1.249 1.287 -0.038 1.90e-02 2.77e+03 4.00e+00 bond pdb=" CA 4J2 L 4 " pdb=" C 4J2 L 4 " ideal model delta sigma weight residual 1.525 1.559 -0.034 2.10e-02 2.27e+03 2.64e+00 bond pdb=" CG1 ILE R 178 " pdb=" CD1 ILE R 178 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.53e+00 bond pdb=" CG1 ILE R 144 " pdb=" CD1 ILE R 144 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.49e+00 bond pdb=" CB THR R 143 " pdb=" CG2 THR R 143 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.87e+00 ... (remaining 8217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.51: 11121 7.51 - 15.01: 2 15.01 - 22.52: 0 22.52 - 30.02: 0 30.02 - 37.53: 1 Bond angle restraints: 11124 Sorted by residual: angle pdb=" CB ASP L 2 " pdb=" CG ASP L 2 " pdb=" OD1 ASP L 2 " ideal model delta sigma weight residual 118.40 80.87 37.53 2.30e+00 1.89e-01 2.66e+02 angle pdb=" N ILE R 178 " pdb=" CA ILE R 178 " pdb=" C ILE R 178 " ideal model delta sigma weight residual 113.71 109.76 3.95 9.50e-01 1.11e+00 1.73e+01 angle pdb=" C ARG N 98 " pdb=" N CYS N 99 " pdb=" CA CYS N 99 " ideal model delta sigma weight residual 123.65 116.01 7.64 1.88e+00 2.83e-01 1.65e+01 angle pdb=" N TRP R 251 " pdb=" CA TRP R 251 " pdb=" C TRP R 251 " ideal model delta sigma weight residual 110.61 115.59 -4.98 1.25e+00 6.40e-01 1.59e+01 angle pdb=" C ILE B 58 " pdb=" N TYR B 59 " pdb=" CA TYR B 59 " ideal model delta sigma weight residual 122.23 116.01 6.22 1.57e+00 4.06e-01 1.57e+01 ... (remaining 11119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4398 17.52 - 35.05: 411 35.05 - 52.57: 71 52.57 - 70.09: 11 70.09 - 87.61: 8 Dihedral angle restraints: 4899 sinusoidal: 1923 harmonic: 2976 Sorted by residual: dihedral pdb=" CH3 ACE L 0 " pdb=" C ACE L 0 " pdb=" N NLE L 1 " pdb=" CA NLE L 1 " ideal model delta sinusoidal sigma weight residual -180.00 -119.60 -60.40 1 5.00e+00 4.00e-02 1.94e+02 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -8.62 -77.38 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CA TRP R 251 " pdb=" C TRP R 251 " pdb=" N ALA R 252 " pdb=" CA ALA R 252 " ideal model delta harmonic sigma weight residual 180.00 145.68 34.32 0 5.00e+00 4.00e-02 4.71e+01 ... (remaining 4896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 864 0.042 - 0.084: 295 0.084 - 0.127: 76 0.127 - 0.169: 17 0.169 - 0.211: 4 Chirality restraints: 1256 Sorted by residual: chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA TRP R 251 " pdb=" N TRP R 251 " pdb=" C TRP R 251 " pdb=" CB TRP R 251 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CA ASN A 195 " pdb=" N ASN A 195 " pdb=" C ASN A 195 " pdb=" CB ASN A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.58e-01 ... (remaining 1253 not shown) Planarity restraints: 1411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE L 0 " 0.077 2.00e-02 2.50e+03 2.63e-01 8.68e+02 pdb=" O ACE L 0 " -0.040 2.00e-02 2.50e+03 pdb=" CH3 ACE L 0 " -0.183 2.00e-02 2.50e+03 pdb=" N NLE L 1 " 0.457 2.00e-02 2.50e+03 pdb=" CA NLE L 1 " -0.312 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 251 " 0.025 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP R 251 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP R 251 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP R 251 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 251 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 251 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 251 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 251 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 251 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP R 251 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " 0.052 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO G 60 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " 0.043 5.00e-02 4.00e+02 ... (remaining 1408 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 96 2.61 - 3.18: 7171 3.18 - 3.76: 12962 3.76 - 4.33: 18198 4.33 - 4.90: 29533 Nonbonded interactions: 67960 Sorted by model distance: nonbonded pdb=" CG ASP L 2 " pdb=" NZ LYS L 7 " model vdw 2.038 3.350 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.047 3.040 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.183 3.040 nonbonded pdb=" NH1 ARG B 49 " pdb=" O TYR B 85 " model vdw 2.208 3.120 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.221 3.040 ... (remaining 67955 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: 1.510 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.980 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 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 : 0.005 0.129 8226 Z= 0.246 Angle : 0.799 37.529 11130 Z= 0.445 Chirality : 0.047 0.211 1256 Planarity : 0.009 0.263 1411 Dihedral : 14.071 87.614 2964 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.83 (0.26), residues: 1001 helix: -0.08 (0.26), residues: 396 sheet: -0.53 (0.33), residues: 225 loop : -0.88 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP R 251 HIS 0.017 0.002 HIS B 62 PHE 0.024 0.002 PHE B 151 TYR 0.011 0.002 TYR A 278 ARG 0.006 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.14709 ( 403) hydrogen bonds : angle 6.14164 ( 1152) SS BOND : bond 0.00260 ( 3) SS BOND : angle 1.76333 ( 6) covalent geometry : bond 0.00453 ( 8222) covalent geometry : angle 0.79775 (11124) Misc. bond : bond 0.12946 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.779 Fit side-chains REVERT: G 21 MET cc_start: 0.5680 (ptp) cc_final: 0.5129 (ptp) REVERT: G 44 HIS cc_start: 0.6793 (m-70) cc_final: 0.6557 (t-90) outliers start: 0 outliers final: 1 residues processed: 115 average time/residue: 1.1028 time to fit residues: 136.0940 Evaluate side-chains 93 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 96 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.219482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.178446 restraints weight = 7411.297| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 2.64 r_work: 0.3867 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8226 Z= 0.152 Angle : 0.592 6.880 11130 Z= 0.318 Chirality : 0.043 0.154 1256 Planarity : 0.005 0.070 1411 Dihedral : 5.204 37.499 1122 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.29 % Allowed : 8.01 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.27), residues: 1001 helix: 0.66 (0.26), residues: 394 sheet: -0.34 (0.33), residues: 228 loop : -0.64 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 251 HIS 0.011 0.001 HIS A 324 PHE 0.016 0.002 PHE B 151 TYR 0.010 0.001 TYR R 72 ARG 0.005 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 403) hydrogen bonds : angle 4.93413 ( 1152) SS BOND : bond 0.00308 ( 3) SS BOND : angle 1.75430 ( 6) covalent geometry : bond 0.00348 ( 8222) covalent geometry : angle 0.59103 (11124) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.900 Fit side-chains REVERT: A 256 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6681 (mp) REVERT: B 220 GLN cc_start: 0.6986 (mp10) cc_final: 0.6704 (mp10) REVERT: B 269 ILE cc_start: 0.7805 (pt) cc_final: 0.7056 (tp) REVERT: G 21 MET cc_start: 0.5155 (ptp) cc_final: 0.4740 (ptp) REVERT: G 44 HIS cc_start: 0.6771 (m-70) cc_final: 0.6119 (t-90) REVERT: R 83 MET cc_start: 0.6578 (tpp) cc_final: 0.5827 (ttp) REVERT: R 235 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6895 (tp-100) outliers start: 20 outliers final: 8 residues processed: 110 average time/residue: 0.9750 time to fit residues: 115.5831 Evaluate side-chains 104 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain R residue 235 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 65 optimal weight: 0.1980 chunk 88 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN A 246 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.222102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.178446 restraints weight = 7541.321| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.99 r_work: 0.3950 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8226 Z= 0.116 Angle : 0.525 5.813 11130 Z= 0.283 Chirality : 0.041 0.142 1256 Planarity : 0.004 0.065 1411 Dihedral : 4.905 52.530 1122 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.29 % Allowed : 10.64 % Favored : 87.07 % 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: 0.18 (0.27), residues: 1001 helix: 1.13 (0.27), residues: 394 sheet: -0.27 (0.33), residues: 226 loop : -0.59 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 251 HIS 0.007 0.001 HIS A 324 PHE 0.013 0.001 PHE B 151 TYR 0.010 0.001 TYR R 72 ARG 0.003 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 403) hydrogen bonds : angle 4.56728 ( 1152) SS BOND : bond 0.00241 ( 3) SS BOND : angle 1.56750 ( 6) covalent geometry : bond 0.00257 ( 8222) covalent geometry : angle 0.52344 (11124) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 1.236 Fit side-chains REVERT: B 220 GLN cc_start: 0.6879 (mp10) cc_final: 0.6503 (mp10) REVERT: G 21 MET cc_start: 0.5494 (ptp) cc_final: 0.4859 (mtt) REVERT: G 44 HIS cc_start: 0.6745 (m-70) cc_final: 0.6253 (t-170) REVERT: R 83 MET cc_start: 0.6626 (tpp) cc_final: 0.5898 (ttp) REVERT: R 178 ILE cc_start: 0.6133 (OUTLIER) cc_final: 0.5832 (mt) REVERT: R 297 PHE cc_start: 0.6469 (m-80) cc_final: 0.6117 (m-80) outliers start: 20 outliers final: 8 residues processed: 111 average time/residue: 1.0721 time to fit residues: 127.4812 Evaluate side-chains 100 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 262 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 52 optimal weight: 5.9990 chunk 79 optimal weight: 0.2980 chunk 91 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 31 optimal weight: 0.3980 chunk 75 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN A 246 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.221477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.177474 restraints weight = 7461.901| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.59 r_work: 0.3921 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8226 Z= 0.120 Angle : 0.519 5.731 11130 Z= 0.280 Chirality : 0.041 0.144 1256 Planarity : 0.004 0.058 1411 Dihedral : 4.530 24.143 1120 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.63 % Allowed : 13.16 % Favored : 84.21 % 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 (0.27), residues: 1001 helix: 1.31 (0.27), residues: 392 sheet: -0.33 (0.33), residues: 227 loop : -0.61 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 251 HIS 0.006 0.001 HIS A 324 PHE 0.013 0.001 PHE B 151 TYR 0.009 0.001 TYR R 72 ARG 0.002 0.000 ARG R 298 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 403) hydrogen bonds : angle 4.49826 ( 1152) SS BOND : bond 0.00272 ( 3) SS BOND : angle 1.52736 ( 6) covalent geometry : bond 0.00271 ( 8222) covalent geometry : angle 0.51798 (11124) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: B 96 ARG cc_start: 0.7900 (mtp180) cc_final: 0.7385 (mmp-170) REVERT: B 220 GLN cc_start: 0.6812 (mp10) cc_final: 0.5517 (tm-30) REVERT: B 222 PHE cc_start: 0.5862 (m-80) cc_final: 0.5537 (m-80) REVERT: G 21 MET cc_start: 0.5576 (ptp) cc_final: 0.4789 (mtt) REVERT: G 44 HIS cc_start: 0.6916 (m-70) cc_final: 0.6160 (t-170) REVERT: N 117 TYR cc_start: 0.5169 (OUTLIER) cc_final: 0.3559 (p90) REVERT: R 83 MET cc_start: 0.6676 (tpp) cc_final: 0.5913 (ttp) REVERT: R 178 ILE cc_start: 0.6225 (OUTLIER) cc_final: 0.5866 (mt) REVERT: R 285 MET cc_start: 0.7383 (ttm) cc_final: 0.7148 (mtp) REVERT: R 297 PHE cc_start: 0.6486 (m-80) cc_final: 0.6156 (m-80) outliers start: 23 outliers final: 11 residues processed: 110 average time/residue: 1.0905 time to fit residues: 129.1423 Evaluate side-chains 107 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 284 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 0.0060 chunk 55 optimal weight: 0.0060 chunk 4 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.221708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.177185 restraints weight = 7364.819| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.57 r_work: 0.3928 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8226 Z= 0.115 Angle : 0.507 5.731 11130 Z= 0.273 Chirality : 0.041 0.144 1256 Planarity : 0.004 0.054 1411 Dihedral : 4.450 24.564 1120 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.75 % Allowed : 15.33 % Favored : 81.92 % 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: 0.33 (0.27), residues: 1001 helix: 1.41 (0.27), residues: 392 sheet: -0.34 (0.33), residues: 227 loop : -0.57 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 251 HIS 0.006 0.001 HIS A 324 PHE 0.012 0.001 PHE B 151 TYR 0.009 0.001 TYR R 72 ARG 0.005 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 403) hydrogen bonds : angle 4.42393 ( 1152) SS BOND : bond 0.00229 ( 3) SS BOND : angle 1.46664 ( 6) covalent geometry : bond 0.00259 ( 8222) covalent geometry : angle 0.50604 (11124) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 235 GLU cc_start: 0.5791 (OUTLIER) cc_final: 0.5214 (mm-30) REVERT: A 353 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6819 (tmm) REVERT: B 96 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7484 (mmp-170) REVERT: B 220 GLN cc_start: 0.6871 (mp10) cc_final: 0.5559 (tm-30) REVERT: B 222 PHE cc_start: 0.5966 (m-80) cc_final: 0.5656 (m-80) REVERT: G 21 MET cc_start: 0.5458 (ptp) cc_final: 0.4801 (mtt) REVERT: G 44 HIS cc_start: 0.6902 (m-70) cc_final: 0.6185 (t-170) REVERT: N 117 TYR cc_start: 0.5327 (OUTLIER) cc_final: 0.3433 (p90) REVERT: R 43 PHE cc_start: 0.6005 (OUTLIER) cc_final: 0.5356 (t80) REVERT: R 83 MET cc_start: 0.6717 (tpp) cc_final: 0.5938 (ttp) REVERT: R 178 ILE cc_start: 0.6182 (OUTLIER) cc_final: 0.5811 (mt) REVERT: R 285 MET cc_start: 0.7389 (ttm) cc_final: 0.7092 (mtp) REVERT: R 297 PHE cc_start: 0.6485 (m-80) cc_final: 0.6156 (m-80) outliers start: 24 outliers final: 10 residues processed: 111 average time/residue: 0.9729 time to fit residues: 116.1930 Evaluate side-chains 106 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 284 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 0.9990 chunk 25 optimal weight: 30.0000 chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.218715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.163157 restraints weight = 7413.409| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.20 r_work: 0.3895 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8226 Z= 0.166 Angle : 0.567 6.104 11130 Z= 0.305 Chirality : 0.043 0.161 1256 Planarity : 0.004 0.053 1411 Dihedral : 4.685 24.906 1120 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.97 % Allowed : 16.59 % Favored : 80.43 % 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: 0.17 (0.27), residues: 1001 helix: 1.20 (0.26), residues: 392 sheet: -0.39 (0.33), residues: 229 loop : -0.59 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 251 HIS 0.008 0.001 HIS A 324 PHE 0.020 0.002 PHE B 151 TYR 0.012 0.002 TYR R 72 ARG 0.004 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 403) hydrogen bonds : angle 4.60137 ( 1152) SS BOND : bond 0.00335 ( 3) SS BOND : angle 1.62503 ( 6) covalent geometry : bond 0.00388 ( 8222) covalent geometry : angle 0.56594 (11124) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 235 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5348 (mm-30) REVERT: B 96 ARG cc_start: 0.8189 (mtp180) cc_final: 0.7579 (mmp-170) REVERT: B 220 GLN cc_start: 0.6969 (mp10) cc_final: 0.5868 (tm-30) REVERT: G 21 MET cc_start: 0.5176 (ptp) cc_final: 0.4744 (mtt) REVERT: G 44 HIS cc_start: 0.6971 (m-70) cc_final: 0.6102 (t-170) REVERT: N 117 TYR cc_start: 0.5264 (OUTLIER) cc_final: 0.3083 (p90) REVERT: R 43 PHE cc_start: 0.6229 (OUTLIER) cc_final: 0.5447 (t80) REVERT: R 83 MET cc_start: 0.6878 (tpp) cc_final: 0.6095 (ttp) REVERT: R 178 ILE cc_start: 0.6512 (OUTLIER) cc_final: 0.6058 (mt) REVERT: R 235 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6914 (tp-100) REVERT: R 285 MET cc_start: 0.7505 (ttm) cc_final: 0.7180 (mtp) REVERT: R 297 PHE cc_start: 0.6449 (m-80) cc_final: 0.6141 (m-80) outliers start: 26 outliers final: 14 residues processed: 111 average time/residue: 0.9377 time to fit residues: 112.8688 Evaluate side-chains 110 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 235 GLN Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 284 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 95 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.218722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.162528 restraints weight = 7434.824| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 1.94 r_work: 0.3912 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8226 Z= 0.159 Angle : 0.563 6.419 11130 Z= 0.303 Chirality : 0.043 0.174 1256 Planarity : 0.004 0.051 1411 Dihedral : 4.700 24.570 1120 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.32 % Allowed : 17.16 % Favored : 79.52 % 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: 0.16 (0.27), residues: 1001 helix: 1.14 (0.26), residues: 394 sheet: -0.38 (0.34), residues: 230 loop : -0.54 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 251 HIS 0.007 0.001 HIS A 324 PHE 0.021 0.002 PHE A 199 TYR 0.012 0.001 TYR R 72 ARG 0.004 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 403) hydrogen bonds : angle 4.61251 ( 1152) SS BOND : bond 0.00311 ( 3) SS BOND : angle 1.56750 ( 6) covalent geometry : bond 0.00370 ( 8222) covalent geometry : angle 0.56237 (11124) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.834 Fit side-chains REVERT: A 235 GLU cc_start: 0.5914 (OUTLIER) cc_final: 0.5328 (mm-30) REVERT: B 96 ARG cc_start: 0.8186 (mtp180) cc_final: 0.7609 (mmp-170) REVERT: B 220 GLN cc_start: 0.6959 (mp10) cc_final: 0.5845 (tm-30) REVERT: G 21 MET cc_start: 0.5061 (ptp) cc_final: 0.4486 (mtt) REVERT: G 44 HIS cc_start: 0.6980 (m-70) cc_final: 0.6094 (t-170) REVERT: N 117 TYR cc_start: 0.5325 (OUTLIER) cc_final: 0.3143 (p90) REVERT: R 43 PHE cc_start: 0.6270 (OUTLIER) cc_final: 0.5540 (t80) REVERT: R 83 MET cc_start: 0.6854 (tpp) cc_final: 0.6059 (ttp) REVERT: R 178 ILE cc_start: 0.6475 (OUTLIER) cc_final: 0.6007 (mt) REVERT: R 235 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6869 (tp-100) REVERT: R 285 MET cc_start: 0.7467 (ttm) cc_final: 0.7160 (mtp) REVERT: R 290 MET cc_start: 0.6284 (tpp) cc_final: 0.5852 (mmm) REVERT: R 297 PHE cc_start: 0.6444 (m-80) cc_final: 0.6130 (m-80) outliers start: 29 outliers final: 15 residues processed: 109 average time/residue: 0.9682 time to fit residues: 113.9048 Evaluate side-chains 110 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 235 GLN Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 284 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.219634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.175533 restraints weight = 7495.282| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.69 r_work: 0.3910 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8226 Z= 0.144 Angle : 0.565 6.711 11130 Z= 0.305 Chirality : 0.042 0.168 1256 Planarity : 0.004 0.050 1411 Dihedral : 4.779 36.774 1120 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.55 % Allowed : 17.05 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.27), residues: 1001 helix: 1.24 (0.26), residues: 394 sheet: -0.47 (0.33), residues: 230 loop : -0.53 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 251 HIS 0.007 0.001 HIS A 324 PHE 0.021 0.002 PHE A 199 TYR 0.013 0.001 TYR R 72 ARG 0.003 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 403) hydrogen bonds : angle 4.55657 ( 1152) SS BOND : bond 0.01163 ( 3) SS BOND : angle 3.86707 ( 6) covalent geometry : bond 0.00332 ( 8222) covalent geometry : angle 0.55781 (11124) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.895 Fit side-chains REVERT: A 235 GLU cc_start: 0.5658 (OUTLIER) cc_final: 0.5024 (mm-30) REVERT: A 256 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6551 (mp) REVERT: B 96 ARG cc_start: 0.8151 (mtp180) cc_final: 0.7565 (mmp-170) REVERT: B 218 CYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7453 (t) REVERT: B 220 GLN cc_start: 0.6965 (mp10) cc_final: 0.5639 (tm-30) REVERT: B 222 PHE cc_start: 0.5825 (m-80) cc_final: 0.5507 (m-80) REVERT: G 21 MET cc_start: 0.4998 (ptp) cc_final: 0.4415 (mtt) REVERT: N 117 TYR cc_start: 0.5450 (OUTLIER) cc_final: 0.3260 (p90) REVERT: R 43 PHE cc_start: 0.6064 (OUTLIER) cc_final: 0.5335 (t80) REVERT: R 83 MET cc_start: 0.6851 (tpp) cc_final: 0.6054 (ttp) REVERT: R 178 ILE cc_start: 0.6364 (OUTLIER) cc_final: 0.5897 (mt) REVERT: R 235 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6865 (tp-100) REVERT: R 285 MET cc_start: 0.7449 (ttm) cc_final: 0.7103 (mtp) REVERT: R 297 PHE cc_start: 0.6401 (m-80) cc_final: 0.6077 (m-80) outliers start: 31 outliers final: 15 residues processed: 106 average time/residue: 0.9866 time to fit residues: 112.7839 Evaluate side-chains 108 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 235 GLN Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 284 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.2132 > 50: distance: 33 - 50: 3.100 distance: 39 - 60: 3.054 distance: 71 - 99: 21.812 distance: 91 - 121: 17.879 distance: 95 - 99: 20.787 distance: 96 - 129: 31.966 distance: 99 - 100: 20.498 distance: 100 - 101: 5.181 distance: 100 - 103: 3.426 distance: 101 - 102: 17.539 distance: 101 - 110: 11.602 distance: 103 - 104: 20.259 distance: 104 - 105: 29.677 distance: 105 - 106: 18.131 distance: 106 - 107: 7.279 distance: 107 - 108: 17.364 distance: 107 - 109: 7.954 distance: 110 - 111: 9.579 distance: 111 - 112: 24.190 distance: 112 - 113: 11.334 distance: 115 - 116: 9.654 distance: 115 - 117: 15.484 distance: 116 - 118: 10.538 distance: 117 - 119: 6.962 distance: 119 - 120: 15.366 distance: 121 - 122: 24.004 distance: 122 - 123: 35.914 distance: 122 - 125: 19.491 distance: 123 - 124: 39.608 distance: 123 - 129: 51.866 distance: 125 - 126: 10.364 distance: 126 - 127: 14.798 distance: 127 - 128: 31.742 distance: 129 - 130: 31.211 distance: 130 - 133: 19.248 distance: 131 - 132: 39.943 distance: 133 - 134: 32.754 distance: 135 - 136: 4.748 distance: 136 - 137: 11.914 distance: 136 - 139: 41.507 distance: 137 - 138: 4.990 distance: 137 - 145: 18.581 distance: 138 - 172: 41.817 distance: 139 - 140: 12.677 distance: 140 - 141: 8.568 distance: 140 - 142: 15.120 distance: 141 - 143: 8.042 distance: 142 - 144: 12.978 distance: 145 - 146: 17.866 distance: 146 - 147: 17.519 distance: 146 - 149: 11.218 distance: 147 - 148: 16.263 distance: 147 - 156: 15.046 distance: 148 - 184: 30.655 distance: 149 - 150: 18.693 distance: 150 - 151: 6.325 distance: 150 - 152: 17.272 distance: 151 - 153: 30.162 distance: 152 - 154: 33.340 distance: 153 - 155: 14.567 distance: 154 - 155: 37.053 distance: 156 - 157: 4.108 distance: 157 - 158: 17.575 distance: 157 - 160: 15.416 distance: 158 - 159: 9.979 distance: 158 - 164: 22.108 distance: 159 - 192: 15.219 distance: 160 - 161: 26.442 distance: 161 - 162: 12.280 distance: 161 - 163: 19.870 distance: 164 - 165: 14.252 distance: 165 - 166: 22.945 distance: 165 - 168: 8.128 distance: 166 - 167: 10.680 distance: 166 - 172: 35.262 distance: 167 - 199: 25.653 distance: 168 - 169: 26.872 distance: 169 - 170: 20.857 distance: 170 - 171: 8.136 distance: 172 - 173: 7.916 distance: 173 - 174: 23.068 distance: 173 - 176: 18.750 distance: 174 - 175: 18.823 distance: 174 - 184: 15.708 distance: 175 - 207: 25.607 distance: 176 - 177: 28.580 distance: 177 - 178: 16.012 distance: 177 - 179: 21.669 distance: 178 - 180: 18.286 distance: 179 - 181: 18.675 distance: 180 - 182: 21.483 distance: 181 - 182: 23.936 distance: 182 - 183: 34.608 distance: 184 - 185: 18.111 distance: 185 - 186: 20.413 distance: 185 - 188: 27.333 distance: 186 - 187: 21.041 distance: 186 - 192: 21.240 distance: 187 - 214: 15.978 distance: 188 - 189: 41.475 distance: 189 - 190: 22.896 distance: 189 - 191: 24.096