Starting phenix.real_space_refine on Fri Nov 15 03:34:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iod_35616/11_2024/8iod_35616.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iod_35616/11_2024/8iod_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iod_35616/11_2024/8iod_35616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iod_35616/11_2024/8iod_35616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iod_35616/11_2024/8iod_35616.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iod_35616/11_2024/8iod_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-5513/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: 5.05, per 1000 atoms: 0.63 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: 2.08 Conformation dependent library (CDL) restraints added in 1.1 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: 0.90 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: 2.35 Time building geometry restraints manager: 2.38 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.000 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.610 ------------------------------------------------------------------------------- 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 0.062 8222 Z= 0.301 Angle : 0.798 37.529 11124 Z= 0.444 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 *********************** 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 : 0.940 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: 1.0730 time to fit residues: 132.4505 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 : 0.852 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 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 8222 Z= 0.231 Angle : 0.591 6.880 11124 Z= 0.318 Chirality : 0.043 0.154 1256 Planarity : 0.005 0.070 1411 Dihedral : 5.204 37.498 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 *********************** 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 : 0.867 Fit side-chains REVERT: A 256 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6706 (mp) REVERT: B 269 ILE cc_start: 0.7856 (pt) cc_final: 0.7083 (tp) REVERT: G 21 MET cc_start: 0.5636 (ptp) cc_final: 0.5048 (ptp) REVERT: R 235 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6642 (tp-100) outliers start: 20 outliers final: 8 residues processed: 110 average time/residue: 1.0519 time to fit residues: 124.5193 Evaluate side-chains 103 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8222 Z= 0.194 Angle : 0.543 6.076 11124 Z= 0.294 Chirality : 0.042 0.143 1256 Planarity : 0.004 0.065 1411 Dihedral : 5.039 53.952 1122 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.40 % Allowed : 10.76 % Favored : 86.84 % 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: 0.10 (0.27), residues: 1001 helix: 1.03 (0.27), residues: 394 sheet: -0.31 (0.33), residues: 227 loop : -0.59 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 251 HIS 0.008 0.001 HIS A 324 PHE 0.014 0.002 PHE B 151 TYR 0.011 0.001 TYR R 72 ARG 0.003 0.000 ARG R 298 *********************** 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 119 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.921 Fit side-chains REVERT: A 256 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6689 (mp) REVERT: G 21 MET cc_start: 0.5933 (ptp) cc_final: 0.4930 (mtt) REVERT: R 178 ILE cc_start: 0.6152 (OUTLIER) cc_final: 0.5925 (mt) outliers start: 21 outliers final: 13 residues processed: 110 average time/residue: 1.0075 time to fit residues: 119.4417 Evaluate side-chains 105 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL 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 N residue 83 MET Chi-restraints excluded: chain R residue 87 MET 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.0970 chunk 61 optimal weight: 10.0000 chunk 91 optimal weight: 0.0070 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 26 optimal weight: 0.0770 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.3154 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8222 Z= 0.144 Angle : 0.498 5.703 11124 Z= 0.269 Chirality : 0.040 0.143 1256 Planarity : 0.004 0.057 1411 Dihedral : 4.463 22.479 1122 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.29 % Allowed : 14.30 % Favored : 83.41 % 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: 0.28 (0.27), residues: 1001 helix: 1.35 (0.27), residues: 394 sheet: -0.34 (0.33), residues: 226 loop : -0.61 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 251 HIS 0.005 0.001 HIS A 324 PHE 0.009 0.001 PHE B 151 TYR 0.009 0.001 TYR R 72 ARG 0.002 0.000 ARG A 209 *********************** 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 114 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: B 269 ILE cc_start: 0.7298 (pt) cc_final: 0.6896 (mp) REVERT: G 21 MET cc_start: 0.6056 (ptp) cc_final: 0.4910 (mtt) REVERT: N 117 TYR cc_start: 0.4809 (OUTLIER) cc_final: 0.3590 (p90) REVERT: R 178 ILE cc_start: 0.6004 (OUTLIER) cc_final: 0.5743 (mt) REVERT: R 285 MET cc_start: 0.7006 (ttm) cc_final: 0.6775 (mtp) outliers start: 20 outliers final: 8 residues processed: 106 average time/residue: 1.0564 time to fit residues: 120.4441 Evaluate side-chains 102 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 43 PHE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain R residue 178 ILE 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 1 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 0.2980 chunk 82 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8222 Z= 0.279 Angle : 0.585 6.639 11124 Z= 0.313 Chirality : 0.043 0.155 1256 Planarity : 0.005 0.056 1411 Dihedral : 4.765 25.916 1120 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.75 % Allowed : 15.45 % Favored : 81.81 % 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 (0.27), residues: 1001 helix: 1.09 (0.26), residues: 392 sheet: -0.45 (0.33), residues: 229 loop : -0.66 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 251 HIS 0.009 0.001 HIS A 324 PHE 0.020 0.002 PHE B 151 TYR 0.011 0.002 TYR R 72 ARG 0.005 0.000 ARG A 209 *********************** 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 120 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 353 MET cc_start: 0.6157 (OUTLIER) cc_final: 0.5764 (tmm) REVERT: G 21 MET cc_start: 0.6040 (ptp) cc_final: 0.4929 (mtt) REVERT: N 117 TYR cc_start: 0.5286 (OUTLIER) cc_final: 0.3660 (p90) REVERT: R 178 ILE cc_start: 0.6398 (OUTLIER) cc_final: 0.6152 (mt) REVERT: R 285 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6842 (mtp) outliers start: 24 outliers final: 12 residues processed: 111 average time/residue: 1.0960 time to fit residues: 130.6078 Evaluate side-chains 108 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 206 ASP 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 87 MET Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 261 MET Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 285 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 0.0570 chunk 10 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8222 Z= 0.172 Angle : 0.522 6.114 11124 Z= 0.280 Chirality : 0.041 0.151 1256 Planarity : 0.004 0.050 1411 Dihedral : 4.493 23.221 1120 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.86 % Allowed : 16.93 % Favored : 80.21 % 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: 0.28 (0.27), residues: 1001 helix: 1.36 (0.27), residues: 394 sheet: -0.34 (0.33), residues: 226 loop : -0.63 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 251 HIS 0.005 0.001 HIS A 324 PHE 0.016 0.001 PHE A 199 TYR 0.010 0.001 TYR R 72 ARG 0.004 0.000 ARG A 209 *********************** 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 121 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 353 MET cc_start: 0.6022 (OUTLIER) cc_final: 0.5638 (tmm) REVERT: G 21 MET cc_start: 0.5976 (ptp) cc_final: 0.5064 (mtt) REVERT: N 117 TYR cc_start: 0.5291 (OUTLIER) cc_final: 0.3613 (p90) REVERT: R 43 PHE cc_start: 0.5949 (OUTLIER) cc_final: 0.5616 (t80) REVERT: R 178 ILE cc_start: 0.6076 (OUTLIER) cc_final: 0.5790 (mt) REVERT: R 235 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6566 (tp-100) REVERT: R 285 MET cc_start: 0.7002 (ttm) cc_final: 0.6656 (mtp) outliers start: 25 outliers final: 12 residues processed: 109 average time/residue: 1.0446 time to fit residues: 122.4123 Evaluate side-chains 108 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 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 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 96 ILE Chi-restraints excluded: chain R residue 106 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 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 55 optimal weight: 0.0970 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8222 Z= 0.237 Angle : 0.556 6.503 11124 Z= 0.300 Chirality : 0.042 0.154 1256 Planarity : 0.004 0.050 1411 Dihedral : 4.643 24.325 1120 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.43 % Allowed : 17.28 % 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: 0.16 (0.27), residues: 1001 helix: 1.23 (0.26), residues: 392 sheet: -0.44 (0.33), residues: 230 loop : -0.60 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 251 HIS 0.007 0.001 HIS A 324 PHE 0.019 0.002 PHE A 199 TYR 0.012 0.001 TYR R 72 ARG 0.008 0.000 ARG A 209 *********************** 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 122 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 353 MET cc_start: 0.6138 (OUTLIER) cc_final: 0.5723 (tmm) REVERT: B 218 CYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6853 (t) REVERT: G 21 MET cc_start: 0.5630 (ptp) cc_final: 0.4725 (mtt) REVERT: N 117 TYR cc_start: 0.5056 (OUTLIER) cc_final: 0.3281 (p90) REVERT: R 43 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5832 (t80) REVERT: R 178 ILE cc_start: 0.6347 (OUTLIER) cc_final: 0.6093 (mt) REVERT: R 235 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6588 (tp-100) outliers start: 30 outliers final: 15 residues processed: 111 average time/residue: 1.0213 time to fit residues: 122.3965 Evaluate side-chains 111 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 286 THR 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 B residue 214 ARG 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 42 VAL Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 87 MET 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 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 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 61 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 84 optimal weight: 0.2980 chunk 89 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 N 82 GLN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8222 Z= 0.160 Angle : 0.515 6.934 11124 Z= 0.278 Chirality : 0.041 0.140 1256 Planarity : 0.004 0.049 1411 Dihedral : 4.412 21.590 1120 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.20 % Allowed : 18.19 % Favored : 78.60 % 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: 0.40 (0.27), residues: 1001 helix: 1.50 (0.27), residues: 394 sheet: -0.33 (0.33), residues: 227 loop : -0.56 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 251 HIS 0.005 0.001 HIS A 324 PHE 0.018 0.001 PHE A 199 TYR 0.014 0.001 TYR N 60 ARG 0.006 0.000 ARG A 209 *********************** 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: 28 poor density : 91 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.4090 (OUTLIER) cc_final: 0.3850 (ttp) REVERT: A 353 MET cc_start: 0.5998 (OUTLIER) cc_final: 0.5614 (tmm) REVERT: B 218 CYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6622 (t) REVERT: G 21 MET cc_start: 0.5599 (ptp) cc_final: 0.4721 (mtt) REVERT: N 83 MET cc_start: 0.4717 (mtp) cc_final: 0.4271 (mtm) REVERT: N 84 ASN cc_start: 0.5873 (OUTLIER) cc_final: 0.5434 (m-40) REVERT: N 117 TYR cc_start: 0.4951 (OUTLIER) cc_final: 0.3247 (p90) REVERT: R 43 PHE cc_start: 0.6139 (OUTLIER) cc_final: 0.5786 (t80) REVERT: R 178 ILE cc_start: 0.6072 (OUTLIER) cc_final: 0.5753 (mt) REVERT: R 235 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.6589 (tp-100) REVERT: R 285 MET cc_start: 0.6988 (ttm) cc_final: 0.6651 (mtp) outliers start: 28 outliers final: 15 residues processed: 107 average time/residue: 1.0348 time to fit residues: 119.1136 Evaluate side-chains 113 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET 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 239 ASP Chi-restraints excluded: chain A residue 286 THR 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 B residue 214 ARG Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 84 ASN 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 96 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 282 ILE Chi-restraints excluded: chain R residue 284 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 57 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 N 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8222 Z= 0.192 Angle : 0.541 8.223 11124 Z= 0.291 Chirality : 0.041 0.174 1256 Planarity : 0.004 0.049 1411 Dihedral : 4.460 22.494 1120 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.09 % Allowed : 18.19 % Favored : 78.72 % 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 (0.27), residues: 1001 helix: 1.48 (0.26), residues: 392 sheet: -0.32 (0.33), residues: 228 loop : -0.56 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 251 HIS 0.006 0.001 HIS A 324 PHE 0.020 0.002 PHE A 199 TYR 0.014 0.001 TYR N 60 ARG 0.007 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 9 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: 27 poor density : 88 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.4178 (OUTLIER) cc_final: 0.3912 (ttp) REVERT: A 353 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.5636 (tmm) REVERT: B 218 CYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6861 (t) REVERT: G 21 MET cc_start: 0.5604 (ptp) cc_final: 0.4727 (mtt) REVERT: N 117 TYR cc_start: 0.5092 (OUTLIER) cc_final: 0.3260 (p90) REVERT: R 43 PHE cc_start: 0.6197 (OUTLIER) cc_final: 0.5849 (t80) REVERT: R 178 ILE cc_start: 0.6180 (OUTLIER) cc_final: 0.5877 (mt) REVERT: R 235 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6582 (tp-100) REVERT: R 285 MET cc_start: 0.7029 (ttm) cc_final: 0.6718 (mtp) outliers start: 27 outliers final: 13 residues processed: 105 average time/residue: 0.9562 time to fit residues: 108.5468 Evaluate side-chains 108 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 286 THR 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 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 42 VAL Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 96 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 282 ILE Chi-restraints excluded: chain R residue 284 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 0.0870 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8222 Z= 0.181 Angle : 0.534 9.200 11124 Z= 0.287 Chirality : 0.041 0.171 1256 Planarity : 0.004 0.049 1411 Dihedral : 4.429 21.920 1120 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.40 % Allowed : 18.76 % Favored : 78.83 % 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 (0.27), residues: 1001 helix: 1.52 (0.27), residues: 392 sheet: -0.33 (0.33), residues: 228 loop : -0.60 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 251 HIS 0.006 0.001 HIS A 324 PHE 0.013 0.001 PHE B 222 TYR 0.015 0.001 TYR N 60 ARG 0.005 0.000 ARG A 209 ********************** REFINEMENT MACRO_CYCLE 10 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 111 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.4170 (OUTLIER) cc_final: 0.3882 (ttp) REVERT: A 217 ASP cc_start: 0.7000 (m-30) cc_final: 0.6767 (m-30) REVERT: A 353 MET cc_start: 0.6043 (OUTLIER) cc_final: 0.5621 (tmm) REVERT: B 218 CYS cc_start: 0.7313 (OUTLIER) cc_final: 0.7042 (t) REVERT: G 21 MET cc_start: 0.5593 (ptp) cc_final: 0.4787 (mpt) REVERT: N 117 TYR cc_start: 0.4973 (OUTLIER) cc_final: 0.3126 (p90) REVERT: R 43 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.5829 (t80) REVERT: R 178 ILE cc_start: 0.6153 (OUTLIER) cc_final: 0.5845 (mt) REVERT: R 235 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6577 (tp-100) REVERT: R 285 MET cc_start: 0.7001 (ttm) cc_final: 0.6683 (mtp) REVERT: R 290 MET cc_start: 0.6354 (tpp) cc_final: 0.5889 (mmm) outliers start: 21 outliers final: 13 residues processed: 102 average time/residue: 1.0538 time to fit residues: 115.7633 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 : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 286 THR 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 B residue 214 ARG 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 42 VAL Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 96 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 282 ILE Chi-restraints excluded: chain R residue 284 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** 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 = 0.4658 r_free = 0.4658 target = 0.220250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.164959 restraints weight = 7462.553| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.93 r_work: 0.3944 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8222 Z= 0.205 Angle : 0.549 9.633 11124 Z= 0.295 Chirality : 0.041 0.151 1256 Planarity : 0.004 0.049 1411 Dihedral : 4.523 23.645 1120 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.63 % Allowed : 18.65 % Favored : 78.72 % 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: 0.34 (0.27), residues: 1001 helix: 1.45 (0.26), residues: 392 sheet: -0.34 (0.33), residues: 228 loop : -0.62 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.007 0.001 HIS A 324 PHE 0.015 0.002 PHE A 199 TYR 0.016 0.001 TYR R 72 ARG 0.004 0.000 ARG A 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3727.78 seconds wall clock time: 67 minutes 49.71 seconds (4069.71 seconds total)