Starting phenix.real_space_refine on Mon Mar 11 10:46:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iod_35616/03_2024/8iod_35616_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iod_35616/03_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_35616/03_2024/8iod_35616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iod_35616/03_2024/8iod_35616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iod_35616/03_2024/8iod_35616_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iod_35616/03_2024/8iod_35616_updated.pdb" } 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 "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "L ASP 2": not complete - not flipped Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8061 Number of models: 1 Model: "" Number of chains: 7 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 75 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 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: "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: 4.94, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.5 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... running ksdssp... Secondary structure from input PDB file: 27 helices and 11 sheets defined 36.3% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.658A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 275 through 278 No H-bonds generated for 'chain 'A' and resid 275 through 278' Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 299 through 318 removed outlier: 3.524A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 357 Processing helix chain 'B' and resid 6 through 24 Processing helix chain 'G' and resid 12 through 23 Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 40 through 43 Processing helix chain 'R' and resid 45 through 59 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 70 through 100 Processing helix chain 'R' and resid 108 through 145 Processing helix chain 'R' and resid 156 through 179 removed outlier: 4.399A pdb=" N ILE R 178 " --> pdb=" O GLY R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 219 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 234 through 246 Processing helix chain 'R' and resid 248 through 251 No H-bonds generated for 'chain 'R' and resid 248 through 251' Processing helix chain 'R' and resid 253 through 260 Processing helix chain 'R' and resid 268 through 295 removed outlier: 3.583A pdb=" N PHE R 273 " --> pdb=" O TYR R 269 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS R 276 " --> pdb=" O ARG R 272 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE R 277 " --> pdb=" O PHE R 273 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASN R 278 " --> pdb=" O MET R 274 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) 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 300 through 311 Processing sheet with id= A, first strand: chain 'A' and resid 326 through 330 removed outlier: 7.533A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.831A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) 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= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.009A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) 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: 3.630A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 151 Processing sheet with id= E, first strand: chain 'B' and resid 221 through 223 removed outlier: 4.544A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.840A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) 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= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.408A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (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= H, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.767A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 166 through 170 removed outlier: 5.746A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= J, 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= K, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.823A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 1032 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: 2.31 Time building geometry restraints manager: 3.41 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: 2030 1.33 - 1.45: 1651 1.45 - 1.57: 4443 1.57 - 1.69: 0 1.69 - 1.82: 99 Bond restraints: 8223 Sorted by residual: bond pdb=" C LYS L 7 " pdb=" N NH2 L 8 " ideal model delta sigma weight residual 1.329 1.301 0.028 1.40e-02 5.10e+03 4.13e+00 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 ... (remaining 8218 not shown) Histogram of bond angle deviations from ideal: 80.87 - 91.50: 1 91.50 - 102.14: 33 102.14 - 112.77: 4484 112.77 - 123.40: 6284 123.40 - 134.04: 324 Bond angle restraints: 11126 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=" CA LYS L 7 " pdb=" C LYS L 7 " pdb=" N NH2 L 8 " ideal model delta sigma weight residual 116.20 101.22 14.98 2.00e+00 2.50e-01 5.61e+01 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=" O LYS L 7 " pdb=" C LYS L 7 " pdb=" N NH2 L 8 " ideal model delta sigma weight residual 123.00 129.49 -6.49 1.60e+00 3.91e-01 1.65e+01 ... (remaining 11121 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: 1412 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=" CA LYS L 7 " -0.041 2.00e-02 2.50e+03 9.54e-02 9.09e+01 pdb=" C LYS L 7 " 0.164 2.00e-02 2.50e+03 pdb=" O LYS L 7 " -0.068 2.00e-02 2.50e+03 pdb=" N NH2 L 8 " -0.055 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 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 100 2.61 - 3.18: 7189 3.18 - 3.76: 13012 3.76 - 4.33: 18298 4.33 - 4.90: 29553 Nonbonded interactions: 68152 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 2.440 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.183 2.440 nonbonded pdb=" NH1 ARG B 49 " pdb=" O TYR B 85 " model vdw 2.208 2.520 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.221 2.440 ... (remaining 68147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 4.000 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.720 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.890 ------------------------------------------------------------------------------- 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 8223 Z= 0.306 Angle : 0.813 37.529 11126 Z= 0.452 Chirality : 0.047 0.211 1256 Planarity : 0.009 0.263 1412 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 fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.947 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: 1.0264 time to fit residues: 126.7036 Evaluate side-chains 93 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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: 0.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 216 ASN A 231 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8223 Z= 0.244 Angle : 0.580 6.792 11126 Z= 0.309 Chirality : 0.044 0.148 1256 Planarity : 0.005 0.068 1412 Dihedral : 5.240 37.094 1122 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.29 % Allowed : 8.35 % Favored : 89.36 % 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 (0.26), residues: 1001 helix: 0.51 (0.27), residues: 392 sheet: -0.36 (0.33), residues: 225 loop : -0.73 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 251 HIS 0.012 0.001 HIS A 324 PHE 0.018 0.002 PHE B 151 TYR 0.009 0.001 TYR R 269 ARG 0.003 0.000 ARG R 298 *********************** 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 117 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.883 Fit side-chains REVERT: A 256 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6842 (mp) REVERT: B 220 GLN cc_start: 0.7146 (mp10) cc_final: 0.6877 (mp10) REVERT: B 269 ILE cc_start: 0.7761 (pt) cc_final: 0.7037 (tp) REVERT: G 21 MET cc_start: 0.5633 (ptp) cc_final: 0.5046 (ptp) REVERT: R 235 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6606 (tp-100) outliers start: 20 outliers final: 7 residues processed: 105 average time/residue: 0.9824 time to fit residues: 111.2094 Evaluate side-chains 101 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 A residue 301 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain R residue 94 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: 0.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 231 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: 0.6385 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8223 Z= 0.224 Angle : 0.546 6.389 11126 Z= 0.293 Chirality : 0.042 0.144 1256 Planarity : 0.004 0.064 1412 Dihedral : 4.993 45.147 1120 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.75 % Allowed : 11.67 % Favored : 85.58 % 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 (0.26), residues: 1001 helix: 0.64 (0.27), residues: 400 sheet: -0.25 (0.33), residues: 224 loop : -0.69 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 251 HIS 0.010 0.001 HIS A 324 PHE 0.017 0.002 PHE B 151 TYR 0.008 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 125 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 0.848 Fit side-chains REVERT: A 256 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6680 (mp) REVERT: B 220 GLN cc_start: 0.7149 (mp10) cc_final: 0.6923 (mp10) REVERT: G 21 MET cc_start: 0.5897 (ptp) cc_final: 0.4888 (mtt) REVERT: R 178 ILE cc_start: 0.6277 (OUTLIER) cc_final: 0.6065 (mt) outliers start: 24 outliers final: 11 residues processed: 111 average time/residue: 1.0514 time to fit residues: 125.4954 Evaluate side-chains 107 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 A residue 301 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.2980 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 26 optimal weight: 0.0270 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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: 0.6331 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8223 Z= 0.161 Angle : 0.496 5.792 11126 Z= 0.267 Chirality : 0.041 0.142 1256 Planarity : 0.004 0.057 1412 Dihedral : 4.547 24.377 1120 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.52 % Allowed : 14.53 % Favored : 82.95 % 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: 0.09 (0.27), residues: 1001 helix: 0.96 (0.27), residues: 399 sheet: -0.19 (0.33), residues: 226 loop : -0.62 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 251 HIS 0.007 0.001 HIS A 324 PHE 0.012 0.001 PHE B 151 TYR 0.010 0.001 TYR N 60 ARG 0.003 0.000 ARG R 298 *********************** 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 122 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.850 Fit side-chains REVERT: B 220 GLN cc_start: 0.7074 (mp10) cc_final: 0.6811 (mp10) REVERT: G 21 MET cc_start: 0.6035 (ptp) cc_final: 0.4847 (mtt) REVERT: N 117 TYR cc_start: 0.4896 (OUTLIER) cc_final: 0.3530 (p90) REVERT: R 43 PHE cc_start: 0.6033 (OUTLIER) cc_final: 0.5753 (t80) REVERT: R 178 ILE cc_start: 0.6204 (OUTLIER) cc_final: 0.5970 (mt) REVERT: R 285 MET cc_start: 0.7062 (ttm) cc_final: 0.6820 (mtp) outliers start: 22 outliers final: 8 residues processed: 112 average time/residue: 1.0267 time to fit residues: 123.6614 Evaluate side-chains 105 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 301 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 43 PHE 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 262 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 0.0030 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 204 GLN A 216 ASN A 231 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8223 Z= 0.197 Angle : 0.512 5.826 11126 Z= 0.275 Chirality : 0.041 0.140 1256 Planarity : 0.004 0.055 1412 Dihedral : 4.536 24.516 1120 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.32 % Allowed : 15.90 % Favored : 80.78 % 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: 0.14 (0.27), residues: 1001 helix: 1.01 (0.27), residues: 399 sheet: -0.20 (0.33), residues: 227 loop : -0.58 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 251 HIS 0.008 0.001 HIS A 324 PHE 0.016 0.002 PHE A 199 TYR 0.011 0.001 TYR N 60 ARG 0.002 0.000 ARG R 298 *********************** 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 128 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.4183 (OUTLIER) cc_final: 0.3909 (ttp) REVERT: A 353 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5693 (tmm) REVERT: B 220 GLN cc_start: 0.6989 (mp10) cc_final: 0.6754 (mp10) REVERT: G 21 MET cc_start: 0.6046 (ptp) cc_final: 0.4920 (mtt) REVERT: N 117 TYR cc_start: 0.5099 (OUTLIER) cc_final: 0.3477 (p90) REVERT: R 43 PHE cc_start: 0.6052 (OUTLIER) cc_final: 0.5741 (t80) REVERT: R 178 ILE cc_start: 0.6261 (OUTLIER) cc_final: 0.6016 (mt) REVERT: R 187 ILE cc_start: 0.6076 (mm) cc_final: 0.5678 (mm) REVERT: R 285 MET cc_start: 0.7065 (ttm) cc_final: 0.6767 (mtp) outliers start: 29 outliers final: 12 residues processed: 115 average time/residue: 1.0652 time to fit residues: 131.6425 Evaluate side-chains 109 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 191 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 301 VAL 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 221 THR Chi-restraints excluded: chain L residue 5 ARG Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 243 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 96 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.0870 chunk 50 optimal weight: 0.0370 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 204 GLN A 216 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: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8223 Z= 0.171 Angle : 0.501 6.182 11126 Z= 0.267 Chirality : 0.041 0.140 1256 Planarity : 0.004 0.052 1412 Dihedral : 4.442 24.076 1120 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.97 % Allowed : 17.16 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 1001 helix: 1.10 (0.27), residues: 400 sheet: -0.14 (0.34), residues: 227 loop : -0.55 (0.33), residues: 374 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 0.017 0.001 PHE A 199 TYR 0.015 0.001 TYR R 280 ARG 0.003 0.000 ARG A 232 *********************** 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 122 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.4181 (OUTLIER) cc_final: 0.3885 (ttp) REVERT: A 353 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5586 (tmm) REVERT: B 218 CYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6843 (t) REVERT: G 21 MET cc_start: 0.5910 (ptp) cc_final: 0.5131 (mtt) REVERT: N 117 TYR cc_start: 0.5271 (OUTLIER) cc_final: 0.3606 (p90) REVERT: R 43 PHE cc_start: 0.6122 (OUTLIER) cc_final: 0.5785 (t80) REVERT: R 178 ILE cc_start: 0.6199 (OUTLIER) cc_final: 0.5964 (mt) REVERT: R 187 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5655 (mm) REVERT: R 285 MET cc_start: 0.6978 (ttm) cc_final: 0.6694 (mtp) outliers start: 26 outliers final: 10 residues processed: 111 average time/residue: 1.0265 time to fit residues: 122.2950 Evaluate side-chains 109 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 206 ASP Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 301 VAL 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 218 CYS Chi-restraints excluded: chain L residue 5 ARG Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 282 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 204 GLN A 216 ASN A 231 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8223 Z= 0.238 Angle : 0.546 6.337 11126 Z= 0.292 Chirality : 0.042 0.142 1256 Planarity : 0.004 0.052 1412 Dihedral : 4.634 24.957 1120 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.20 % Allowed : 17.28 % 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: 0.14 (0.27), residues: 1001 helix: 0.97 (0.26), residues: 399 sheet: -0.15 (0.34), residues: 225 loop : -0.57 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.009 0.001 HIS A 324 PHE 0.021 0.002 PHE A 199 TYR 0.014 0.001 TYR N 60 ARG 0.002 0.000 ARG B 134 *********************** 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 fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 0.917 Fit side-chains REVERT: A 18 MET cc_start: 0.4290 (OUTLIER) cc_final: 0.3989 (ttp) REVERT: A 353 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5767 (tmm) REVERT: B 218 CYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7023 (t) REVERT: G 21 MET cc_start: 0.5692 (ptp) cc_final: 0.4736 (mtt) REVERT: L 5 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7621 (mmt180) REVERT: N 117 TYR cc_start: 0.4903 (OUTLIER) cc_final: 0.3215 (p90) REVERT: R 43 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.5861 (t80) REVERT: R 178 ILE cc_start: 0.6373 (OUTLIER) cc_final: 0.6131 (mt) REVERT: R 235 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6574 (tp-100) REVERT: R 285 MET cc_start: 0.7057 (ttm) cc_final: 0.6827 (mtp) outliers start: 28 outliers final: 14 residues processed: 106 average time/residue: 0.9915 time to fit residues: 113.3576 Evaluate side-chains 111 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 191 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 301 VAL 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 218 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain L residue 5 ARG Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 43 PHE 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 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: 0.9980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8223 Z= 0.171 Angle : 0.509 6.836 11126 Z= 0.271 Chirality : 0.040 0.139 1256 Planarity : 0.004 0.049 1412 Dihedral : 4.445 23.108 1120 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.43 % Allowed : 17.62 % Favored : 78.95 % 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: 1.16 (0.27), residues: 400 sheet: -0.15 (0.34), residues: 227 loop : -0.54 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 251 HIS 0.006 0.001 HIS A 324 PHE 0.020 0.001 PHE A 199 TYR 0.013 0.001 TYR N 60 ARG 0.003 0.000 ARG B 134 *********************** 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 123 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 0.902 Fit side-chains REVERT: A 18 MET cc_start: 0.4167 (OUTLIER) cc_final: 0.3869 (ttp) REVERT: A 353 MET cc_start: 0.5991 (OUTLIER) cc_final: 0.5578 (tmm) REVERT: B 218 CYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7036 (t) REVERT: G 21 MET cc_start: 0.5605 (ptp) cc_final: 0.4721 (mtt) REVERT: L 5 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7589 (mmt180) REVERT: N 117 TYR cc_start: 0.5126 (OUTLIER) cc_final: 0.3374 (p90) REVERT: R 43 PHE cc_start: 0.6214 (OUTLIER) cc_final: 0.5855 (t80) REVERT: R 178 ILE cc_start: 0.6191 (OUTLIER) cc_final: 0.5987 (mt) REVERT: R 235 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6572 (tp-100) REVERT: R 285 MET cc_start: 0.6966 (ttm) cc_final: 0.6712 (mtp) REVERT: R 290 MET cc_start: 0.6319 (tpp) cc_final: 0.5850 (mmm) outliers start: 30 outliers final: 12 residues processed: 110 average time/residue: 0.9709 time to fit residues: 115.1583 Evaluate side-chains 112 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 206 ASP Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 301 VAL 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 218 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain L residue 5 ARG Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 43 PHE 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 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: 0.5980 chunk 54 optimal weight: 0.0980 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 0.0000 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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** N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8223 Z= 0.158 Angle : 0.502 7.574 11126 Z= 0.268 Chirality : 0.041 0.156 1256 Planarity : 0.004 0.050 1412 Dihedral : 4.368 27.176 1120 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.75 % Allowed : 18.88 % Favored : 78.38 % 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: 1.26 (0.27), residues: 400 sheet: -0.10 (0.34), residues: 227 loop : -0.49 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 251 HIS 0.006 0.001 HIS A 324 PHE 0.020 0.001 PHE A 199 TYR 0.015 0.001 TYR N 60 ARG 0.002 0.000 ARG R 140 *********************** 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 120 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.4128 (OUTLIER) cc_final: 0.3835 (ttp) REVERT: A 353 MET cc_start: 0.5979 (OUTLIER) cc_final: 0.5544 (tmm) REVERT: B 218 CYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6974 (t) REVERT: G 21 MET cc_start: 0.5580 (ptp) cc_final: 0.4728 (mtt) REVERT: N 117 TYR cc_start: 0.5055 (OUTLIER) cc_final: 0.3304 (p90) REVERT: R 43 PHE cc_start: 0.6200 (OUTLIER) cc_final: 0.5829 (t80) REVERT: R 178 ILE cc_start: 0.6076 (OUTLIER) cc_final: 0.5859 (mt) REVERT: R 187 ILE cc_start: 0.6032 (mm) cc_final: 0.5628 (mm) REVERT: R 235 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6572 (tp-100) REVERT: R 285 MET cc_start: 0.6926 (ttm) cc_final: 0.6638 (mtp) outliers start: 24 outliers final: 13 residues processed: 109 average time/residue: 0.9692 time to fit residues: 114.5462 Evaluate side-chains 110 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 206 ASP Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 301 VAL 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 218 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain L residue 5 ARG Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 235 GLN 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: 0.5980 chunk 66 optimal weight: 0.0030 chunk 99 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 231 ASN A 246 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8223 Z= 0.174 Angle : 0.517 9.202 11126 Z= 0.275 Chirality : 0.041 0.168 1256 Planarity : 0.004 0.050 1412 Dihedral : 4.411 25.331 1120 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.75 % Allowed : 18.76 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 1001 helix: 1.26 (0.27), residues: 400 sheet: -0.12 (0.34), residues: 227 loop : -0.55 (0.32), residues: 374 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 0.011 0.001 PHE B 151 TYR 0.014 0.001 TYR N 60 ARG 0.009 0.000 ARG B 134 ********************** 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 112 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 0.816 Fit side-chains REVERT: A 18 MET cc_start: 0.4157 (OUTLIER) cc_final: 0.3884 (ttp) REVERT: A 353 MET cc_start: 0.6061 (OUTLIER) cc_final: 0.5632 (tmm) REVERT: B 218 CYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6983 (t) REVERT: G 21 MET cc_start: 0.5576 (ptp) cc_final: 0.4795 (mpt) REVERT: L 5 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7542 (mmt180) REVERT: N 117 TYR cc_start: 0.4821 (OUTLIER) cc_final: 0.3316 (p90) REVERT: R 43 PHE cc_start: 0.6218 (OUTLIER) cc_final: 0.5881 (t80) REVERT: R 178 ILE cc_start: 0.6127 (OUTLIER) cc_final: 0.5926 (mt) REVERT: R 187 ILE cc_start: 0.6063 (OUTLIER) cc_final: 0.5696 (mm) REVERT: R 235 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6561 (tp-100) REVERT: R 285 MET cc_start: 0.6925 (ttm) cc_final: 0.6674 (mtp) outliers start: 24 outliers final: 12 residues processed: 101 average time/residue: 0.9823 time to fit residues: 106.9664 Evaluate side-chains 109 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 206 ASP Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 301 VAL 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 218 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain L residue 5 ARG Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 235 GLN 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: 0.6980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 0.0570 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- 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 231 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 = 0.4661 r_free = 0.4661 target = 0.220998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.177390 restraints weight = 7441.263| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.67 r_work: 0.3923 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8223 Z= 0.195 Angle : 0.532 9.920 11126 Z= 0.282 Chirality : 0.041 0.158 1256 Planarity : 0.004 0.050 1412 Dihedral : 4.466 26.359 1120 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.09 % Allowed : 18.65 % Favored : 78.26 % 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: 1.21 (0.26), residues: 400 sheet: -0.10 (0.34), residues: 227 loop : -0.53 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 251 HIS 0.007 0.001 HIS A 324 PHE 0.016 0.002 PHE A 199 TYR 0.014 0.001 TYR N 60 ARG 0.009 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3488.66 seconds wall clock time: 62 minutes 41.82 seconds (3761.82 seconds total)