Starting phenix.real_space_refine on Fri Jul 19 11:54:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jr9_36593/07_2024/8jr9_36593_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jr9_36593/07_2024/8jr9_36593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jr9_36593/07_2024/8jr9_36593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jr9_36593/07_2024/8jr9_36593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jr9_36593/07_2024/8jr9_36593_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jr9_36593/07_2024/8jr9_36593_neut_trim.cif" } resolution = 2.57 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= 0.000 sd= 0.002 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 S 48 5.16 5 C 5027 2.51 5 N 1346 2.21 5 O 1469 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 186": not complete - not flipped Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7893 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1917 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2547 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "G" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 389 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "N" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 969 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 123} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2027 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 250} Chain breaks: 3 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 6, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 56 Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'KHF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.00, per 1000 atoms: 0.63 Number of scatterers: 7893 At special positions: 0 Unit cell: (92.288, 108.768, 106.296, 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) S 48 16.00 F 3 9.00 O 1469 8.00 N 1346 7.00 C 5027 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 281 " - pdb=" SG CYS R 351 " distance=2.10 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: 3.45 Conformation dependent library (CDL) restraints added in 1.6 seconds 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 42.7% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 5 through 33 removed outlier: 4.007A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 54 through 57 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.558A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.833A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.517A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 22 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.033A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 112 removed outlier: 4.495A pdb=" N THR N 111 " --> pdb=" O PHE N 108 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER N 112 " --> pdb=" O ASP N 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 108 through 112' Processing helix chain 'R' and resid 186 through 212 removed outlier: 3.566A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 243 Processing helix chain 'R' and resid 278 through 312 removed outlier: 3.624A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 356 through 359 Processing helix chain 'R' and resid 360 through 393 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 414 Processing helix chain 'R' and resid 415 through 427 removed outlier: 4.366A pdb=" N VAL R 419 " --> pdb=" O PRO R 415 " (cutoff:3.500A) Processing helix chain 'R' and resid 437 through 460 removed outlier: 4.914A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 481 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.441A pdb=" N VAL A 224 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLY A 40 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG A 35 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE A 245 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 37 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL A 247 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU A 39 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ASP A 249 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.611A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.524A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.981A 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: 6.778A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.657A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.825A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.878A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.582A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.577A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.929A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1191 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: 2.23 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1286 1.30 - 1.43: 2203 1.43 - 1.56: 4509 1.56 - 1.68: 1 1.68 - 1.81: 65 Bond restraints: 8064 Sorted by residual: bond pdb=" C16 KHF R 601 " pdb=" N2 KHF R 601 " ideal model delta sigma weight residual 1.274 1.458 -0.184 2.00e-02 2.50e+03 8.46e+01 bond pdb=" C25 KHF R 601 " pdb=" N4 KHF R 601 " ideal model delta sigma weight residual 1.353 1.455 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C12 KHF R 601 " pdb=" C13 KHF R 601 " ideal model delta sigma weight residual 1.530 1.429 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C13 KHF R 601 " pdb=" C14 KHF R 601 " ideal model delta sigma weight residual 1.532 1.440 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C TYR B 145 " pdb=" N LEU B 146 " ideal model delta sigma weight residual 1.331 1.275 0.055 1.41e-02 5.03e+03 1.54e+01 ... (remaining 8059 not shown) Histogram of bond angle deviations from ideal: 90.48 - 99.18: 1 99.18 - 107.89: 244 107.89 - 116.59: 5273 116.59 - 125.29: 5299 125.29 - 134.00: 142 Bond angle restraints: 10959 Sorted by residual: angle pdb=" C12 KHF R 601 " pdb=" C13 KHF R 601 " pdb=" N2 KHF R 601 " ideal model delta sigma weight residual 110.89 133.09 -22.20 3.00e+00 1.11e-01 5.48e+01 angle pdb=" C14 KHF R 601 " pdb=" C13 KHF R 601 " pdb=" N2 KHF R 601 " ideal model delta sigma weight residual 110.23 90.48 19.75 3.00e+00 1.11e-01 4.33e+01 angle pdb=" O1 KHF R 601 " pdb=" S1 KHF R 601 " pdb=" O2 KHF R 601 " ideal model delta sigma weight residual 118.72 101.40 17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" O TYR B 145 " pdb=" C TYR B 145 " pdb=" N LEU B 146 " ideal model delta sigma weight residual 122.89 116.90 5.99 1.22e+00 6.72e-01 2.41e+01 angle pdb=" N GLN A 294 " pdb=" CA GLN A 294 " pdb=" C GLN A 294 " ideal model delta sigma weight residual 113.23 107.35 5.88 1.24e+00 6.50e-01 2.25e+01 ... (remaining 10954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 4361 25.08 - 50.15: 344 50.15 - 75.23: 38 75.23 - 100.31: 2 100.31 - 125.39: 10 Dihedral angle restraints: 4755 sinusoidal: 1805 harmonic: 2950 Sorted by residual: dihedral pdb=" CA ASP B 186 " pdb=" CB ASP B 186 " pdb=" CG ASP B 186 " pdb=" OD1 ASP B 186 " ideal model delta sinusoidal sigma weight residual 70.00 175.51 -105.51 1 2.00e+01 2.50e-03 3.04e+01 dihedral pdb=" C25 KHF R 601 " pdb=" C27 KHF R 601 " pdb=" N4 KHF R 601 " pdb=" C29 KHF R 601 " ideal model delta sinusoidal sigma weight residual 116.77 -117.84 -125.39 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C28 KHF R 601 " pdb=" C27 KHF R 601 " pdb=" N4 KHF R 601 " pdb=" C4 KHF R 601 " ideal model delta sinusoidal sigma weight residual -64.48 60.62 -125.10 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 4752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 993 0.045 - 0.090: 181 0.090 - 0.135: 57 0.135 - 0.180: 2 0.180 - 0.225: 4 Chirality restraints: 1237 Sorted by residual: chirality pdb=" CA LEU B 190 " pdb=" N LEU B 190 " pdb=" C LEU B 190 " pdb=" CB LEU B 190 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL R 243 " pdb=" N VAL R 243 " pdb=" C VAL R 243 " pdb=" CB VAL R 243 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1234 not shown) Planarity restraints: 1387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C THR B 87 " -0.030 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 332 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 145 " 0.007 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C TYR B 145 " -0.023 2.00e-02 2.50e+03 pdb=" O TYR B 145 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU B 146 " 0.008 2.00e-02 2.50e+03 ... (remaining 1384 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1471 2.77 - 3.30: 7376 3.30 - 3.84: 13547 3.84 - 4.37: 15152 4.37 - 4.90: 26951 Nonbonded interactions: 64497 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.240 2.440 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.247 2.440 nonbonded pdb=" O VAL R 423 " pdb=" OG1 THR R 427 " model vdw 2.254 2.440 nonbonded pdb=" O THR A 325 " pdb=" OG1 THR A 325 " model vdw 2.260 2.440 nonbonded pdb=" OG SER B 97 " pdb=" OD2 ASP B 118 " model vdw 2.305 2.440 ... (remaining 64492 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: 1.170 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.650 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: 0.000 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 0.184 8064 Z= 0.324 Angle : 0.649 22.198 10959 Z= 0.337 Chirality : 0.040 0.225 1237 Planarity : 0.003 0.041 1387 Dihedral : 17.649 125.387 2838 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.24 % Allowed : 24.85 % Favored : 74.91 % 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: 1.80 (0.27), residues: 994 helix: 2.79 (0.26), residues: 400 sheet: 0.86 (0.36), residues: 206 loop : -0.32 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.004 0.000 HIS A 387 PHE 0.014 0.001 PHE R 238 TYR 0.009 0.001 TYR R 191 ARG 0.007 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 0.861 Fit side-chains REVERT: A 14 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6317 (pp20) REVERT: A 15 ARG cc_start: 0.6178 (ttt-90) cc_final: 0.5290 (ttm110) REVERT: A 21 LYS cc_start: 0.7531 (mtpt) cc_final: 0.6548 (tptp) REVERT: A 213 GLN cc_start: 0.7928 (mt0) cc_final: 0.7427 (tt0) REVERT: A 221 MET cc_start: 0.7744 (ptp) cc_final: 0.7421 (ttp) REVERT: A 240 ASP cc_start: 0.5941 (p0) cc_final: 0.5720 (p0) REVERT: A 268 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6501 (tp30) REVERT: A 347 ARG cc_start: 0.7238 (ptp90) cc_final: 0.6813 (ptp-170) REVERT: A 380 ARG cc_start: 0.7733 (ttm110) cc_final: 0.7263 (ttm110) REVERT: A 389 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7326 (mtm110) REVERT: B 90 VAL cc_start: 0.7823 (m) cc_final: 0.7602 (p) REVERT: B 97 SER cc_start: 0.7018 (p) cc_final: 0.6716 (t) REVERT: B 155 ASN cc_start: 0.6327 (t0) cc_final: 0.6086 (t0) REVERT: B 226 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7037 (mt-10) REVERT: B 325 MET cc_start: 0.8175 (tpp) cc_final: 0.7853 (tpp) REVERT: N 113 THR cc_start: 0.8213 (p) cc_final: 0.7979 (t) REVERT: R 189 MET cc_start: 0.6914 (tpt) cc_final: 0.6519 (tpp) outliers start: 2 outliers final: 1 residues processed: 198 average time/residue: 0.9780 time to fit residues: 207.5406 Evaluate side-chains 126 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 264 ASN B 75 GLN B 119 ASN B 176 GLN B 295 ASN G 44 HIS N 5 GLN N 35 ASN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN R 467 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8064 Z= 0.304 Angle : 0.613 6.992 10959 Z= 0.327 Chirality : 0.044 0.156 1237 Planarity : 0.004 0.049 1387 Dihedral : 12.708 126.711 1145 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.75 % Allowed : 20.56 % Favored : 73.68 % 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: 1.92 (0.27), residues: 994 helix: 2.84 (0.25), residues: 398 sheet: 0.98 (0.34), residues: 218 loop : -0.28 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 329 HIS 0.011 0.002 HIS A 357 PHE 0.017 0.002 PHE A 363 TYR 0.025 0.002 TYR A 339 ARG 0.007 0.001 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 152 time to evaluate : 0.960 Fit side-chains REVERT: A 14 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6497 (pp20) REVERT: A 15 ARG cc_start: 0.6386 (ttt-90) cc_final: 0.5596 (ttp80) REVERT: A 21 LYS cc_start: 0.7607 (mtpt) cc_final: 0.6718 (pptt) REVERT: A 24 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.6628 (mp10) REVERT: A 25 LYS cc_start: 0.7922 (ttmm) cc_final: 0.7418 (mttp) REVERT: A 28 GLN cc_start: 0.7096 (mt0) cc_final: 0.6590 (mm-40) REVERT: A 213 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: A 236 GLN cc_start: 0.8502 (mt0) cc_final: 0.8230 (mt0) REVERT: A 240 ASP cc_start: 0.6644 (p0) cc_final: 0.6336 (p0) REVERT: A 276 ILE cc_start: 0.8057 (mt) cc_final: 0.7816 (mm) REVERT: A 370 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: A 389 ARG cc_start: 0.7845 (tpp-160) cc_final: 0.7375 (mtm110) REVERT: B 90 VAL cc_start: 0.8009 (m) cc_final: 0.7642 (p) REVERT: B 142 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.8234 (m170) REVERT: B 146 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8158 (mm) REVERT: B 170 ASP cc_start: 0.7673 (p0) cc_final: 0.7261 (p0) REVERT: B 197 ARG cc_start: 0.7173 (tpp-160) cc_final: 0.6445 (mmt90) REVERT: B 226 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7927 (mt-10) REVERT: N 70 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8196 (tt) REVERT: R 189 MET cc_start: 0.6938 (tpt) cc_final: 0.6523 (tpp) REVERT: R 207 LEU cc_start: 0.7030 (mt) cc_final: 0.6721 (mm) REVERT: R 312 MET cc_start: 0.6847 (ptp) cc_final: 0.6571 (ptp) outliers start: 47 outliers final: 10 residues processed: 181 average time/residue: 1.0827 time to fit residues: 209.3283 Evaluate side-chains 145 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 0.0170 chunk 74 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS A 264 ASN A 271 ASN A 279 ASN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN R 467 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8064 Z= 0.164 Angle : 0.483 8.006 10959 Z= 0.258 Chirality : 0.039 0.142 1237 Planarity : 0.003 0.039 1387 Dihedral : 12.562 127.326 1142 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 4.65 % Allowed : 22.40 % Favored : 72.95 % 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: 2.19 (0.27), residues: 994 helix: 3.17 (0.25), residues: 398 sheet: 1.21 (0.34), residues: 212 loop : -0.30 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.023 0.001 PHE R 327 TYR 0.012 0.001 TYR R 297 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 0.954 Fit side-chains REVERT: A 14 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6424 (pp20) REVERT: A 15 ARG cc_start: 0.6389 (ttt-90) cc_final: 0.5607 (ttp80) REVERT: A 21 LYS cc_start: 0.7548 (mtpt) cc_final: 0.6534 (tptp) REVERT: A 28 GLN cc_start: 0.7229 (mt0) cc_final: 0.6684 (mm-40) REVERT: A 213 GLN cc_start: 0.8589 (mt0) cc_final: 0.8149 (tt0) REVERT: A 236 GLN cc_start: 0.8686 (mt0) cc_final: 0.8417 (mt0) REVERT: A 240 ASP cc_start: 0.6794 (p0) cc_final: 0.6496 (p0) REVERT: A 268 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6527 (tp30) REVERT: A 276 ILE cc_start: 0.7996 (mt) cc_final: 0.7732 (mm) REVERT: A 389 ARG cc_start: 0.7837 (tpp-160) cc_final: 0.7366 (mtm110) REVERT: B 90 VAL cc_start: 0.7836 (m) cc_final: 0.7482 (p) REVERT: B 146 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8118 (mm) REVERT: B 197 ARG cc_start: 0.7096 (tpp-160) cc_final: 0.6378 (mmt90) REVERT: B 314 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7745 (ptt180) REVERT: N 3 GLN cc_start: 0.7547 (pt0) cc_final: 0.7258 (pt0) REVERT: N 70 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8230 (tt) REVERT: R 189 MET cc_start: 0.6938 (tpt) cc_final: 0.6527 (tpp) REVERT: R 312 MET cc_start: 0.6874 (ptp) cc_final: 0.6586 (ptp) outliers start: 38 outliers final: 17 residues processed: 161 average time/residue: 1.1277 time to fit residues: 193.1618 Evaluate side-chains 148 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 390 ARG Chi-restraints excluded: chain R residue 449 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 0.0770 chunk 47 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS A 264 ASN B 142 HIS N 35 ASN R 307 HIS R 364 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8064 Z= 0.128 Angle : 0.446 6.825 10959 Z= 0.236 Chirality : 0.038 0.136 1237 Planarity : 0.003 0.041 1387 Dihedral : 12.382 127.181 1142 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.67 % Allowed : 22.52 % Favored : 73.81 % 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: 2.36 (0.27), residues: 994 helix: 3.33 (0.26), residues: 398 sheet: 1.43 (0.34), residues: 203 loop : -0.27 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE R 327 TYR 0.012 0.001 TYR A 358 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 0.887 Fit side-chains REVERT: A 21 LYS cc_start: 0.7546 (mtpt) cc_final: 0.6565 (tptp) REVERT: A 28 GLN cc_start: 0.7243 (mt0) cc_final: 0.6714 (mm-40) REVERT: A 213 GLN cc_start: 0.8605 (mt0) cc_final: 0.8190 (tt0) REVERT: A 240 ASP cc_start: 0.6742 (p0) cc_final: 0.6507 (p0) REVERT: A 268 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6495 (tp30) REVERT: A 276 ILE cc_start: 0.7947 (mt) cc_final: 0.7695 (mm) REVERT: A 389 ARG cc_start: 0.7827 (tpp-160) cc_final: 0.7323 (mtm110) REVERT: B 90 VAL cc_start: 0.7745 (m) cc_final: 0.7539 (p) REVERT: B 146 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8092 (mm) REVERT: B 170 ASP cc_start: 0.7382 (p0) cc_final: 0.7148 (p0) REVERT: B 197 ARG cc_start: 0.7048 (tpp-160) cc_final: 0.6272 (mmt90) REVERT: B 314 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7916 (ptt180) REVERT: N 3 GLN cc_start: 0.7477 (pt0) cc_final: 0.7197 (pt0) REVERT: N 70 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8261 (tt) REVERT: R 189 MET cc_start: 0.6929 (tpt) cc_final: 0.6517 (tpp) outliers start: 30 outliers final: 15 residues processed: 152 average time/residue: 1.0752 time to fit residues: 174.2914 Evaluate side-chains 138 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 390 ARG Chi-restraints excluded: chain R residue 449 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 220 HIS A 264 ASN A 278 ASN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8064 Z= 0.254 Angle : 0.540 6.366 10959 Z= 0.289 Chirality : 0.041 0.148 1237 Planarity : 0.004 0.044 1387 Dihedral : 12.824 127.757 1142 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.90 % Allowed : 22.03 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.27), residues: 994 helix: 3.10 (0.25), residues: 397 sheet: 1.12 (0.34), residues: 215 loop : -0.35 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.019 0.002 PHE R 327 TYR 0.020 0.002 TYR A 358 ARG 0.004 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 0.882 Fit side-chains REVERT: A 15 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.6334 (ttt-90) REVERT: A 21 LYS cc_start: 0.7598 (mtpt) cc_final: 0.6568 (tptp) REVERT: A 28 GLN cc_start: 0.7210 (mt0) cc_final: 0.6575 (mp10) REVERT: A 55 ILE cc_start: 0.6232 (OUTLIER) cc_final: 0.5888 (pt) REVERT: A 240 ASP cc_start: 0.6942 (p0) cc_final: 0.6737 (p0) REVERT: A 268 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6885 (tt0) REVERT: A 276 ILE cc_start: 0.8049 (mt) cc_final: 0.7828 (mm) REVERT: A 370 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: A 374 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7946 (mtt180) REVERT: A 389 ARG cc_start: 0.7859 (tpp-160) cc_final: 0.7383 (mtm110) REVERT: B 65 THR cc_start: 0.7735 (m) cc_final: 0.7300 (p) REVERT: B 138 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7812 (mt-10) REVERT: B 197 ARG cc_start: 0.7156 (tpp-160) cc_final: 0.6397 (mmt90) REVERT: B 314 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7880 (ptt180) REVERT: N 3 GLN cc_start: 0.7403 (pt0) cc_final: 0.7164 (pt0) REVERT: N 20 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7406 (pp) REVERT: N 70 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8256 (tt) REVERT: R 189 MET cc_start: 0.6894 (tpt) cc_final: 0.6475 (tpp) REVERT: R 198 SER cc_start: 0.7655 (OUTLIER) cc_final: 0.7164 (m) REVERT: R 312 MET cc_start: 0.7273 (ptp) cc_final: 0.7065 (ptp) outliers start: 40 outliers final: 19 residues processed: 154 average time/residue: 1.1368 time to fit residues: 186.1358 Evaluate side-chains 146 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 449 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 220 HIS A 264 ASN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8064 Z= 0.270 Angle : 0.553 7.109 10959 Z= 0.295 Chirality : 0.042 0.148 1237 Planarity : 0.004 0.045 1387 Dihedral : 13.214 141.282 1142 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.24 % Allowed : 20.44 % Favored : 73.32 % 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: 1.87 (0.27), residues: 994 helix: 2.92 (0.26), residues: 397 sheet: 0.97 (0.35), residues: 207 loop : -0.40 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.017 0.002 PHE R 327 TYR 0.018 0.002 TYR A 358 ARG 0.004 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 123 time to evaluate : 0.911 Fit side-chains REVERT: A 15 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.6292 (ttt-90) REVERT: A 21 LYS cc_start: 0.7588 (mtpt) cc_final: 0.6588 (tptp) REVERT: A 24 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6678 (mp10) REVERT: A 28 GLN cc_start: 0.7319 (mt0) cc_final: 0.6685 (mp10) REVERT: A 51 LYS cc_start: 0.7314 (mmtm) cc_final: 0.6971 (mttt) REVERT: A 55 ILE cc_start: 0.6355 (OUTLIER) cc_final: 0.6035 (pt) REVERT: A 213 GLN cc_start: 0.8749 (mt0) cc_final: 0.8448 (tt0) REVERT: A 268 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6850 (tt0) REVERT: A 276 ILE cc_start: 0.8025 (mt) cc_final: 0.7807 (mm) REVERT: A 370 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7151 (pm20) REVERT: A 374 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7975 (mtt180) REVERT: A 389 ARG cc_start: 0.7859 (tpp-160) cc_final: 0.7385 (mtm110) REVERT: B 170 ASP cc_start: 0.7924 (p0) cc_final: 0.7710 (p0) REVERT: B 197 ARG cc_start: 0.7186 (tpp-160) cc_final: 0.6434 (mmt90) REVERT: B 314 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7759 (ptt180) REVERT: N 3 GLN cc_start: 0.7279 (pt0) cc_final: 0.7070 (pt0) REVERT: N 20 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7463 (pp) REVERT: N 70 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8271 (tt) REVERT: R 189 MET cc_start: 0.6911 (tpt) cc_final: 0.6507 (tpp) REVERT: R 198 SER cc_start: 0.7654 (OUTLIER) cc_final: 0.7153 (m) REVERT: R 199 LEU cc_start: 0.8037 (tp) cc_final: 0.7827 (tt) outliers start: 51 outliers final: 21 residues processed: 158 average time/residue: 1.1307 time to fit residues: 189.7979 Evaluate side-chains 153 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 54 optimal weight: 0.0670 chunk 69 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 268 ASN R 307 HIS R 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8064 Z= 0.162 Angle : 0.477 6.419 10959 Z= 0.254 Chirality : 0.039 0.142 1237 Planarity : 0.003 0.045 1387 Dihedral : 13.087 139.855 1142 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.18 % Allowed : 23.26 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.27), residues: 994 helix: 3.12 (0.26), residues: 397 sheet: 1.03 (0.35), residues: 213 loop : -0.27 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE R 327 TYR 0.014 0.001 TYR A 358 ARG 0.004 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 0.816 Fit side-chains REVERT: A 21 LYS cc_start: 0.7642 (mtpt) cc_final: 0.7034 (mptt) REVERT: A 28 GLN cc_start: 0.7249 (mt0) cc_final: 0.6589 (mp10) REVERT: A 55 ILE cc_start: 0.6352 (OUTLIER) cc_final: 0.6077 (pt) REVERT: A 213 GLN cc_start: 0.8710 (mt0) cc_final: 0.8404 (tt0) REVERT: A 268 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6900 (tt0) REVERT: A 389 ARG cc_start: 0.7818 (tpp-160) cc_final: 0.7306 (mtm110) REVERT: B 146 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8042 (mm) REVERT: B 197 ARG cc_start: 0.7183 (tpp-160) cc_final: 0.6440 (mmt90) REVERT: B 228 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8150 (m-30) REVERT: B 314 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7883 (ptt180) REVERT: N 70 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8332 (tt) REVERT: R 189 MET cc_start: 0.6894 (tpt) cc_final: 0.6445 (tpp) outliers start: 26 outliers final: 14 residues processed: 143 average time/residue: 1.2183 time to fit residues: 185.0023 Evaluate side-chains 133 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 HIS R 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8064 Z= 0.171 Angle : 0.480 6.820 10959 Z= 0.255 Chirality : 0.039 0.142 1237 Planarity : 0.003 0.046 1387 Dihedral : 13.050 141.342 1142 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.43 % Allowed : 23.01 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.27), residues: 994 helix: 3.13 (0.25), residues: 397 sheet: 1.01 (0.35), residues: 213 loop : -0.27 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE R 327 TYR 0.014 0.001 TYR A 358 ARG 0.004 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 0.829 Fit side-chains REVERT: A 21 LYS cc_start: 0.7611 (mtpt) cc_final: 0.7021 (mptt) REVERT: A 28 GLN cc_start: 0.7256 (mt0) cc_final: 0.6595 (mp10) REVERT: A 51 LYS cc_start: 0.7240 (mmtm) cc_final: 0.6970 (mttt) REVERT: A 55 ILE cc_start: 0.6364 (OUTLIER) cc_final: 0.6108 (pt) REVERT: A 213 GLN cc_start: 0.8736 (mt0) cc_final: 0.8392 (tt0) REVERT: A 236 GLN cc_start: 0.8617 (mt0) cc_final: 0.8372 (mt0) REVERT: A 268 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6857 (tt0) REVERT: A 389 ARG cc_start: 0.7809 (tpp-160) cc_final: 0.7295 (mtm110) REVERT: B 146 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8059 (mm) REVERT: B 196 THR cc_start: 0.7250 (OUTLIER) cc_final: 0.6999 (p) REVERT: B 197 ARG cc_start: 0.7150 (tpp-160) cc_final: 0.6429 (mmt90) REVERT: B 314 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7900 (ptt180) REVERT: N 20 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7409 (pp) REVERT: N 70 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8347 (tt) REVERT: R 189 MET cc_start: 0.6890 (tpt) cc_final: 0.6452 (tpp) outliers start: 28 outliers final: 14 residues processed: 137 average time/residue: 1.1010 time to fit residues: 160.4694 Evaluate side-chains 142 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 HIS R 364 GLN R 467 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8064 Z= 0.195 Angle : 0.501 6.917 10959 Z= 0.266 Chirality : 0.040 0.145 1237 Planarity : 0.003 0.046 1387 Dihedral : 13.047 143.929 1142 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.43 % Allowed : 23.01 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.27), residues: 994 helix: 3.07 (0.25), residues: 397 sheet: 1.01 (0.35), residues: 213 loop : -0.29 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.001 PHE R 327 TYR 0.018 0.001 TYR A 358 ARG 0.004 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 0.951 Fit side-chains REVERT: A 15 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.6254 (ttt-90) REVERT: A 21 LYS cc_start: 0.7597 (mtpt) cc_final: 0.7021 (mptt) REVERT: A 28 GLN cc_start: 0.7296 (mt0) cc_final: 0.6648 (mp10) REVERT: A 55 ILE cc_start: 0.6341 (OUTLIER) cc_final: 0.6075 (pt) REVERT: A 213 GLN cc_start: 0.8739 (mt0) cc_final: 0.8404 (tt0) REVERT: A 268 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6879 (tt0) REVERT: A 370 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7118 (pm20) REVERT: A 389 ARG cc_start: 0.7791 (tpp-160) cc_final: 0.7293 (mtm110) REVERT: B 146 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8070 (mm) REVERT: B 196 THR cc_start: 0.7228 (OUTLIER) cc_final: 0.6979 (p) REVERT: B 197 ARG cc_start: 0.7181 (tpp-160) cc_final: 0.6447 (mmt90) REVERT: B 314 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7860 (ptt180) REVERT: N 20 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7483 (pp) REVERT: R 189 MET cc_start: 0.6954 (tpt) cc_final: 0.6513 (tpp) outliers start: 28 outliers final: 15 residues processed: 143 average time/residue: 1.2806 time to fit residues: 194.0535 Evaluate side-chains 137 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 0.0170 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 8 optimal weight: 0.0870 chunk 60 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 HIS R 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8064 Z= 0.139 Angle : 0.464 6.749 10959 Z= 0.246 Chirality : 0.039 0.143 1237 Planarity : 0.003 0.046 1387 Dihedral : 12.924 140.845 1142 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.45 % Allowed : 24.24 % Favored : 73.32 % 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: 2.15 (0.27), residues: 994 helix: 3.16 (0.26), residues: 397 sheet: 1.03 (0.35), residues: 213 loop : -0.22 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 387 PHE 0.015 0.001 PHE R 327 TYR 0.014 0.001 TYR A 358 ARG 0.004 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 0.949 Fit side-chains REVERT: A 21 LYS cc_start: 0.7532 (mtpt) cc_final: 0.6975 (mptt) REVERT: A 28 GLN cc_start: 0.7244 (mt0) cc_final: 0.6584 (mp10) REVERT: A 55 ILE cc_start: 0.6350 (OUTLIER) cc_final: 0.6111 (pt) REVERT: A 213 GLN cc_start: 0.8719 (mt0) cc_final: 0.8381 (tt0) REVERT: A 236 GLN cc_start: 0.8607 (mt0) cc_final: 0.8380 (mt0) REVERT: A 268 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6919 (tt0) REVERT: A 356 ARG cc_start: 0.7198 (mtm110) cc_final: 0.6909 (mtm180) REVERT: A 370 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: A 389 ARG cc_start: 0.7753 (tpp-160) cc_final: 0.7251 (mtm110) REVERT: B 196 THR cc_start: 0.7199 (OUTLIER) cc_final: 0.6974 (p) REVERT: B 197 ARG cc_start: 0.7156 (tpp-160) cc_final: 0.6445 (mmt90) REVERT: B 314 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7850 (ptt180) REVERT: R 189 MET cc_start: 0.7029 (tpt) cc_final: 0.6590 (tpp) outliers start: 20 outliers final: 9 residues processed: 137 average time/residue: 1.1549 time to fit residues: 168.3854 Evaluate side-chains 140 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.0060 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 HIS R 364 GLN R 380 ASN R 467 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.181187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.147197 restraints weight = 8521.729| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.51 r_work: 0.3572 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8064 Z= 0.178 Angle : 0.486 7.346 10959 Z= 0.256 Chirality : 0.040 0.153 1237 Planarity : 0.003 0.046 1387 Dihedral : 12.946 141.703 1142 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.82 % Allowed : 24.11 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.27), residues: 994 helix: 3.10 (0.26), residues: 398 sheet: 1.08 (0.36), residues: 212 loop : -0.22 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE R 327 TYR 0.014 0.001 TYR R 297 ARG 0.004 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3549.75 seconds wall clock time: 62 minutes 44.07 seconds (3764.07 seconds total)