Starting phenix.real_space_refine on Thu Jan 18 13:11:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_20285/01_2024/6pb1_20285_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_20285/01_2024/6pb1_20285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_20285/01_2024/6pb1_20285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_20285/01_2024/6pb1_20285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_20285/01_2024/6pb1_20285_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_20285/01_2024/6pb1_20285_updated.pdb" } resolution = 2.8 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5642 2.51 5 N 1507 2.21 5 O 1584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 114": "NH1" <-> "NH2" Residue "P ARG 142": "NH1" <-> "NH2" Residue "P ARG 145": "NH1" <-> "NH2" Residue "P ARG 295": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "N PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8785 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2363 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain: "U" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 330 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "A" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1892 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 202 Unusual residues: {'CLR': 4, 'PLM': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 5.17, per 1000 atoms: 0.59 Number of scatterers: 8785 At special positions: 0 Unit cell: (106.47, 96.33, 137.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1584 8.00 N 1507 7.00 C 5642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS P 184 " - pdb=" SG CYS P 254 " distance=2.03 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=2.02 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: 3.19 Conformation dependent library (CDL) restraints added in 1.7 seconds 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 10 sheets defined 38.4% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'P' and resid 111 through 140 removed outlier: 4.083A pdb=" N ALA P 133 " --> pdb=" O ALA P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 169 Processing helix chain 'P' and resid 174 through 178 Processing helix chain 'P' and resid 182 through 213 Processing helix chain 'P' and resid 224 through 231 Processing helix chain 'P' and resid 234 through 247 Proline residue: P 237 - end of helix removed outlier: 4.233A pdb=" N ALA P 241 " --> pdb=" O ILE P 238 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE P 244 " --> pdb=" O ALA P 241 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU P 247 " --> pdb=" O ILE P 244 " (cutoff:3.500A) Processing helix chain 'P' and resid 253 through 255 No H-bonds generated for 'chain 'P' and resid 253 through 255' Processing helix chain 'P' and resid 264 through 297 removed outlier: 3.867A pdb=" N TYR P 268 " --> pdb=" O ASP P 265 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN P 269 " --> pdb=" O TYR P 266 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY P 270 " --> pdb=" O ILE P 267 " (cutoff:3.500A) Proline residue: P 271 - end of helix removed outlier: 3.631A pdb=" N ARG P 295 " --> pdb=" O THR P 292 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA P 296 " --> pdb=" O LYS P 293 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER P 297 " --> pdb=" O LEU P 294 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 319 Proline residue: P 317 - end of helix Processing helix chain 'P' and resid 321 through 324 Processing helix chain 'P' and resid 334 through 349 removed outlier: 3.678A pdb=" N ILE P 338 " --> pdb=" O ASP P 334 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET P 339 " --> pdb=" O LEU P 335 " (cutoff:3.500A) Processing helix chain 'P' and resid 351 through 360 Processing helix chain 'P' and resid 364 through 381 Processing helix chain 'U' and resid 9 through 39 removed outlier: 3.587A pdb=" N THR U 16 " --> pdb=" O HIS U 12 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU U 17 " --> pdb=" O LEU U 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 39 removed outlier: 4.191A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 349 removed outlier: 4.045A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.664A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 43 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 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.031A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.061A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.034A 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: 6.870A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.833A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.779A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.880A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.025A 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: 6.602A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.812A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.996A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1074 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: 2.70 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2774 1.34 - 1.46: 1744 1.46 - 1.58: 4386 1.58 - 1.70: 0 1.70 - 1.81: 72 Bond restraints: 8976 Sorted by residual: bond pdb=" CA LEU P 171 " pdb=" C LEU P 171 " ideal model delta sigma weight residual 1.523 1.548 -0.024 1.30e-02 5.92e+03 3.51e+00 bond pdb=" C ILE P 234 " pdb=" N PRO P 235 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.86e+00 bond pdb=" CA VAL P 172 " pdb=" C VAL P 172 " ideal model delta sigma weight residual 1.522 1.543 -0.021 1.35e-02 5.49e+03 2.47e+00 bond pdb=" C5 CLR P 401 " pdb=" C6 CLR P 401 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C5 CLR P 403 " pdb=" C6 CLR P 403 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 8971 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.66: 209 106.66 - 113.50: 4926 113.50 - 120.34: 3453 120.34 - 127.19: 3469 127.19 - 134.03: 90 Bond angle restraints: 12147 Sorted by residual: angle pdb=" N VAL P 172 " pdb=" CA VAL P 172 " pdb=" C VAL P 172 " ideal model delta sigma weight residual 109.63 121.67 -12.04 1.44e+00 4.82e-01 6.99e+01 angle pdb=" N LEU P 171 " pdb=" CA LEU P 171 " pdb=" C LEU P 171 " ideal model delta sigma weight residual 111.28 119.28 -8.00 1.09e+00 8.42e-01 5.39e+01 angle pdb=" CA ILE P 234 " pdb=" C ILE P 234 " pdb=" N PRO P 235 " ideal model delta sigma weight residual 118.88 123.00 -4.12 1.54e+00 4.22e-01 7.16e+00 angle pdb=" CA PHE P 236 " pdb=" C PHE P 236 " pdb=" N PRO P 237 " ideal model delta sigma weight residual 118.44 122.67 -4.23 1.59e+00 3.96e-01 7.09e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 122.40 126.21 -3.81 1.45e+00 4.76e-01 6.92e+00 ... (remaining 12142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 5293 15.06 - 30.12: 173 30.12 - 45.18: 47 45.18 - 60.23: 15 60.23 - 75.29: 7 Dihedral angle restraints: 5535 sinusoidal: 2418 harmonic: 3117 Sorted by residual: dihedral pdb=" CA PRO P 235 " pdb=" C PRO P 235 " pdb=" N PHE P 236 " pdb=" CA PHE P 236 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASN N 35 " pdb=" C ASN N 35 " pdb=" N TRP N 36 " pdb=" CA TRP N 36 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA TYR N 60 " pdb=" C TYR N 60 " pdb=" N THR N 61 " pdb=" CA THR N 61 " ideal model delta harmonic sigma weight residual 180.00 164.25 15.75 0 5.00e+00 4.00e-02 9.92e+00 ... (remaining 5532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1216 0.084 - 0.168: 113 0.168 - 0.252: 15 0.252 - 0.336: 3 0.336 - 0.420: 5 Chirality restraints: 1352 Sorted by residual: chirality pdb=" C14 CLR P 403 " pdb=" C13 CLR P 403 " pdb=" C15 CLR P 403 " pdb=" C8 CLR P 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" C14 CLR P 401 " pdb=" C13 CLR P 401 " pdb=" C15 CLR P 401 " pdb=" C8 CLR P 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C14 CLR P 402 " pdb=" C13 CLR P 402 " pdb=" C15 CLR P 402 " pdb=" C8 CLR P 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 1349 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN P 170 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" C GLN P 170 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN P 170 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU P 171 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 314 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C VAL P 314 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL P 314 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU P 315 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 301 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.53e+00 pdb=" C VAL A 301 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL A 301 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 302 " 0.015 2.00e-02 2.50e+03 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2343 2.81 - 3.33: 7350 3.33 - 3.86: 13889 3.86 - 4.38: 16284 4.38 - 4.90: 28560 Nonbonded interactions: 68426 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.288 2.440 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.313 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.335 2.440 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.346 2.520 nonbonded pdb=" OG SER P 297 " pdb=" NH1 ARG A 385 " model vdw 2.371 2.520 ... (remaining 68421 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: 0.670 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: 2.680 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.970 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 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 : 0.003 0.040 8976 Z= 0.223 Angle : 0.788 12.041 12147 Z= 0.421 Chirality : 0.059 0.420 1352 Planarity : 0.006 0.063 1523 Dihedral : 9.366 75.292 3506 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -2.93 (0.20), residues: 1051 helix: -1.45 (0.19), residues: 420 sheet: -1.51 (0.30), residues: 226 loop : -2.58 (0.23), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 169 HIS 0.016 0.002 HIS A 220 PHE 0.026 0.002 PHE P 327 TYR 0.026 0.002 TYR N 115 ARG 0.007 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.113 Fit side-chains REVERT: P 234 ILE cc_start: 0.7291 (mt) cc_final: 0.6944 (mt) REVERT: A 300 LYS cc_start: 0.6362 (mmtt) cc_final: 0.6090 (pptt) REVERT: A 391 TYR cc_start: 0.7778 (m-80) cc_final: 0.7541 (m-80) REVERT: B 188 MET cc_start: 0.7941 (mmm) cc_final: 0.7710 (mmt) REVERT: N 80 TYR cc_start: 0.6023 (m-80) cc_final: 0.5772 (m-80) REVERT: N 110 VAL cc_start: 0.7114 (t) cc_final: 0.6901 (m) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 1.1316 time to fit residues: 290.2284 Evaluate side-chains 146 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.0470 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 152 HIS P 351 GLN P 381 HIS A 23 ASN A 278 ASN A 387 HIS B 266 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8976 Z= 0.199 Angle : 0.525 7.192 12147 Z= 0.270 Chirality : 0.041 0.132 1352 Planarity : 0.004 0.041 1523 Dihedral : 7.178 59.524 1504 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.97 % Allowed : 11.60 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1051 helix: 0.52 (0.23), residues: 427 sheet: -1.09 (0.31), residues: 219 loop : -1.85 (0.25), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.021 0.002 PHE P 358 TYR 0.014 0.001 TYR A 37 ARG 0.003 0.000 ARG P 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 0.902 Fit side-chains REVERT: P 109 TYR cc_start: 0.6628 (OUTLIER) cc_final: 0.5654 (p90) REVERT: P 234 ILE cc_start: 0.7683 (mt) cc_final: 0.7286 (mt) REVERT: U 24 GLN cc_start: 0.7835 (tp40) cc_final: 0.7242 (tp-100) REVERT: U 28 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: A 341 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8358 (mp) REVERT: B 55 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8588 (mt) REVERT: B 96 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6387 (ptp-170) REVERT: B 175 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.6905 (mp10) REVERT: B 234 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: B 280 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7928 (tmtm) REVERT: G 48 ASP cc_start: 0.8164 (t0) cc_final: 0.7877 (t0) outliers start: 37 outliers final: 12 residues processed: 181 average time/residue: 1.1197 time to fit residues: 216.9200 Evaluate side-chains 160 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain U residue 4 SER Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 ASN ** P 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 ASN A 23 ASN A 59 GLN B 88 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8976 Z= 0.294 Angle : 0.552 6.677 12147 Z= 0.288 Chirality : 0.043 0.147 1352 Planarity : 0.004 0.040 1523 Dihedral : 7.610 59.891 1504 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.73 % Allowed : 13.75 % Favored : 81.53 % 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: -0.69 (0.24), residues: 1051 helix: 0.88 (0.25), residues: 429 sheet: -0.96 (0.32), residues: 212 loop : -1.56 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.002 PHE A 212 TYR 0.014 0.002 TYR P 249 ARG 0.004 0.001 ARG P 373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 153 time to evaluate : 1.032 Fit side-chains REVERT: P 109 TYR cc_start: 0.6819 (OUTLIER) cc_final: 0.6318 (p90) REVERT: P 234 ILE cc_start: 0.8262 (mt) cc_final: 0.8014 (mt) REVERT: U 8 ASP cc_start: 0.7846 (t0) cc_final: 0.7575 (t0) REVERT: U 24 GLN cc_start: 0.7894 (tp40) cc_final: 0.7225 (tp-100) REVERT: U 28 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: A 300 LYS cc_start: 0.6872 (mmtt) cc_final: 0.6457 (pttp) REVERT: B 55 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8597 (mt) REVERT: B 96 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6121 (ptp-170) REVERT: B 105 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.8051 (t80) REVERT: B 175 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.6893 (mp10) REVERT: B 234 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: G 38 MET cc_start: 0.7811 (ttp) cc_final: 0.7532 (ttm) REVERT: G 48 ASP cc_start: 0.8236 (t0) cc_final: 0.7928 (t0) REVERT: N 43 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6462 (mtpp) outliers start: 44 outliers final: 24 residues processed: 174 average time/residue: 1.0493 time to fit residues: 196.6783 Evaluate side-chains 171 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 164 VAL Chi-restraints excluded: chain P residue 185 ARG Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 4 SER Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 ASN P 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8976 Z= 0.166 Angle : 0.471 7.067 12147 Z= 0.245 Chirality : 0.040 0.134 1352 Planarity : 0.003 0.035 1523 Dihedral : 7.008 59.191 1504 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.51 % Allowed : 16.11 % Favored : 79.38 % 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: -0.18 (0.25), residues: 1051 helix: 1.42 (0.25), residues: 423 sheet: -0.71 (0.32), residues: 209 loop : -1.40 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE P 256 TYR 0.013 0.001 TYR A 37 ARG 0.009 0.000 ARG P 288 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 147 time to evaluate : 1.104 Fit side-chains REVERT: P 109 TYR cc_start: 0.6728 (OUTLIER) cc_final: 0.6360 (p90) REVERT: U 24 GLN cc_start: 0.7842 (tp40) cc_final: 0.7199 (tp40) REVERT: U 28 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: A 300 LYS cc_start: 0.6835 (mmtt) cc_final: 0.6385 (tttt) REVERT: A 341 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8394 (mp) REVERT: B 17 GLN cc_start: 0.7724 (tp-100) cc_final: 0.7501 (tp-100) REVERT: B 96 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6189 (ptp-170) REVERT: B 105 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7995 (t80) REVERT: B 175 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.6926 (mp10) REVERT: B 234 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: B 259 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.6828 (pm20) REVERT: B 280 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7983 (tmtm) REVERT: G 38 MET cc_start: 0.7762 (ttp) cc_final: 0.7498 (ttm) REVERT: G 48 ASP cc_start: 0.8257 (t0) cc_final: 0.7935 (t0) outliers start: 42 outliers final: 21 residues processed: 166 average time/residue: 0.9979 time to fit residues: 179.1369 Evaluate side-chains 161 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain P residue 324 MET Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 344 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8976 Z= 0.252 Angle : 0.525 7.376 12147 Z= 0.272 Chirality : 0.042 0.154 1352 Planarity : 0.004 0.033 1523 Dihedral : 7.145 55.347 1504 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.59 % Allowed : 15.79 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1051 helix: 1.51 (0.25), residues: 422 sheet: -0.67 (0.32), residues: 211 loop : -1.28 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.002 PHE P 256 TYR 0.014 0.001 TYR A 37 ARG 0.007 0.000 ARG P 288 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 0.869 Fit side-chains REVERT: P 170 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.6461 (mp10) REVERT: U 8 ASP cc_start: 0.7920 (t0) cc_final: 0.7698 (t0) REVERT: U 24 GLN cc_start: 0.7838 (tp40) cc_final: 0.7252 (tp40) REVERT: U 28 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: A 221 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7612 (tpp) REVERT: A 300 LYS cc_start: 0.6930 (mmtt) cc_final: 0.6496 (tttt) REVERT: A 370 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6699 (tt0) REVERT: A 372 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7786 (mp) REVERT: B 17 GLN cc_start: 0.7739 (tp-100) cc_final: 0.7493 (tp-100) REVERT: B 96 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6204 (ptp-170) REVERT: B 105 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.8052 (t80) REVERT: B 175 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.6890 (mp10) REVERT: B 234 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: B 259 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.6782 (pm20) REVERT: B 280 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8106 (tmtm) REVERT: G 38 MET cc_start: 0.7740 (ttp) cc_final: 0.7461 (ttm) REVERT: G 48 ASP cc_start: 0.8271 (t0) cc_final: 0.7948 (t0) REVERT: N 43 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6519 (mtpp) outliers start: 52 outliers final: 27 residues processed: 164 average time/residue: 1.0839 time to fit residues: 190.4596 Evaluate side-chains 169 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 164 VAL Chi-restraints excluded: chain P residue 170 GLN Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain P residue 324 MET Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 8.9990 chunk 19 optimal weight: 0.0040 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8976 Z= 0.183 Angle : 0.490 9.754 12147 Z= 0.254 Chirality : 0.040 0.133 1352 Planarity : 0.003 0.034 1523 Dihedral : 6.808 57.256 1504 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.26 % Allowed : 16.97 % Favored : 77.77 % 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: 0.19 (0.25), residues: 1051 helix: 1.76 (0.25), residues: 419 sheet: -0.55 (0.33), residues: 209 loop : -1.18 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE P 256 TYR 0.012 0.001 TYR A 37 ARG 0.009 0.000 ARG P 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 137 time to evaluate : 1.057 Fit side-chains REVERT: U 24 GLN cc_start: 0.7926 (tp40) cc_final: 0.7344 (tp40) REVERT: U 28 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: A 221 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7643 (tpp) REVERT: A 300 LYS cc_start: 0.6923 (mmtt) cc_final: 0.6488 (tttt) REVERT: A 370 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6713 (tt0) REVERT: A 372 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7771 (mp) REVERT: B 17 GLN cc_start: 0.7737 (tp-100) cc_final: 0.7528 (tp-100) REVERT: B 105 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.8018 (t80) REVERT: B 175 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.6932 (mp10) REVERT: B 234 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: B 259 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.6738 (pm20) REVERT: B 280 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8011 (tmtm) REVERT: G 38 MET cc_start: 0.7703 (ttp) cc_final: 0.7426 (ttm) REVERT: G 48 ASP cc_start: 0.8296 (t0) cc_final: 0.7970 (t0) REVERT: N 82 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6776 (tp40) outliers start: 49 outliers final: 28 residues processed: 161 average time/residue: 1.0910 time to fit residues: 188.3872 Evaluate side-chains 168 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 164 VAL Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain P residue 324 MET Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.0470 chunk 59 optimal weight: 4.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8976 Z= 0.153 Angle : 0.469 8.219 12147 Z= 0.244 Chirality : 0.039 0.133 1352 Planarity : 0.003 0.036 1523 Dihedral : 6.506 57.561 1504 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.05 % Allowed : 18.05 % Favored : 76.91 % 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: 0.39 (0.25), residues: 1051 helix: 1.93 (0.25), residues: 419 sheet: -0.47 (0.33), residues: 209 loop : -1.06 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE P 256 TYR 0.013 0.001 TYR N 60 ARG 0.008 0.000 ARG P 288 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 141 time to evaluate : 0.981 Fit side-chains REVERT: P 170 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.6362 (mp10) REVERT: U 24 GLN cc_start: 0.7896 (tp40) cc_final: 0.7259 (tp40) REVERT: U 28 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: A 221 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7624 (tpp) REVERT: A 300 LYS cc_start: 0.6978 (mmtt) cc_final: 0.6560 (tttt) REVERT: A 370 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6729 (tt0) REVERT: A 372 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7757 (mp) REVERT: B 105 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.8043 (t80) REVERT: B 175 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.6937 (mp10) REVERT: B 234 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: B 259 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.6758 (pm20) REVERT: G 38 MET cc_start: 0.7622 (ttp) cc_final: 0.7338 (ttm) REVERT: G 48 ASP cc_start: 0.8281 (t0) cc_final: 0.7961 (t0) REVERT: N 43 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6518 (mtpp) outliers start: 47 outliers final: 27 residues processed: 165 average time/residue: 1.0507 time to fit residues: 186.8949 Evaluate side-chains 168 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 164 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 170 GLN Chi-restraints excluded: chain P residue 185 ARG Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain P residue 324 MET Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 91 optimal weight: 0.0070 chunk 96 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 30.0000 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 ASN N 82 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8976 Z= 0.155 Angle : 0.478 8.434 12147 Z= 0.248 Chirality : 0.039 0.131 1352 Planarity : 0.003 0.032 1523 Dihedral : 6.369 57.907 1504 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.26 % Allowed : 18.37 % Favored : 76.37 % 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: 0.44 (0.25), residues: 1051 helix: 1.89 (0.25), residues: 427 sheet: -0.42 (0.33), residues: 209 loop : -1.00 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE P 256 TYR 0.012 0.001 TYR N 60 ARG 0.007 0.000 ARG P 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 136 time to evaluate : 0.941 Fit side-chains REVERT: P 170 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.6399 (mp10) REVERT: U 24 GLN cc_start: 0.7979 (tp40) cc_final: 0.7409 (tp40) REVERT: U 28 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: A 221 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7637 (tpp) REVERT: A 300 LYS cc_start: 0.6964 (mmtt) cc_final: 0.6565 (tttt) REVERT: A 370 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6754 (tt0) REVERT: A 372 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7766 (mp) REVERT: B 105 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.8041 (t80) REVERT: B 175 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.6939 (mp10) REVERT: B 234 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: B 259 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.6726 (pm20) REVERT: G 38 MET cc_start: 0.7613 (ttp) cc_final: 0.7323 (ttm) REVERT: G 48 ASP cc_start: 0.8290 (t0) cc_final: 0.7969 (t0) REVERT: N 43 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6494 (mtpp) outliers start: 49 outliers final: 28 residues processed: 164 average time/residue: 1.1087 time to fit residues: 195.3044 Evaluate side-chains 173 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 145 ARG Chi-restraints excluded: chain P residue 164 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 170 GLN Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain P residue 324 MET Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.2947 > 50: distance: 6 - 8: 27.161 distance: 8 - 9: 3.710 distance: 9 - 10: 11.698 distance: 10 - 11: 6.625 distance: 10 - 12: 22.951 distance: 12 - 13: 27.764 distance: 13 - 14: 7.639 distance: 13 - 16: 18.380 distance: 14 - 15: 9.646 distance: 14 - 20: 28.164 distance: 16 - 17: 6.964 distance: 17 - 19: 3.786 distance: 20 - 21: 6.028 distance: 21 - 22: 29.653 distance: 21 - 24: 28.798 distance: 22 - 23: 20.728 distance: 22 - 27: 21.671 distance: 24 - 25: 36.833 distance: 24 - 26: 5.051 distance: 27 - 28: 14.095 distance: 28 - 29: 11.559 distance: 28 - 31: 9.997 distance: 29 - 30: 8.222 distance: 31 - 32: 26.669 distance: 32 - 33: 38.164 distance: 33 - 34: 14.795 distance: 33 - 35: 9.494 distance: 36 - 37: 14.274 distance: 36 - 42: 22.884 distance: 37 - 38: 14.054 distance: 37 - 40: 39.749 distance: 38 - 39: 22.238 distance: 40 - 41: 25.243 distance: 41 - 42: 21.242 distance: 43 - 44: 3.250 distance: 44 - 45: 17.026 distance: 45 - 46: 8.329 distance: 45 - 47: 7.075 distance: 47 - 48: 16.487 distance: 48 - 49: 16.588 distance: 49 - 50: 14.199 distance: 49 - 51: 22.656 distance: 51 - 52: 7.402 distance: 52 - 53: 4.943 distance: 52 - 55: 10.042 distance: 53 - 57: 13.118 distance: 55 - 56: 22.982 distance: 57 - 58: 4.418 distance: 57 - 106: 13.302 distance: 58 - 59: 7.927 distance: 59 - 60: 14.030 distance: 59 - 65: 25.399 distance: 60 - 103: 22.987 distance: 61 - 62: 16.744 distance: 62 - 63: 19.055 distance: 62 - 64: 17.722 distance: 65 - 66: 25.608 distance: 66 - 67: 24.373 distance: 66 - 69: 14.014 distance: 67 - 68: 9.828 distance: 72 - 73: 7.523 distance: 73 - 74: 7.213 distance: 73 - 75: 9.750