Starting phenix.real_space_refine on Fri Dec 8 16:39:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_20285/12_2023/6pb1_20285_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_20285/12_2023/6pb1_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_20285/12_2023/6pb1_20285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_20285/12_2023/6pb1_20285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_20285/12_2023/6pb1_20285_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb1_20285/12_2023/6pb1_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-1.21rc1-5172/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: 5.36, per 1000 atoms: 0.61 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: 3.14 Conformation dependent library (CDL) restraints added in 1.6 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: 1.55 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: 2.32 Time building geometry restraints manager: 3.49 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: 1.500 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: 2.780 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 26.000 Find NCS groups from input model: 0.220 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:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.220 ------------------------------------------------------------------------------- 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 : 0.981 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 1.1359 time to fit residues: 290.9530 Evaluate side-chains 145 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2107 ------------------------------------------------------------------------------- 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: 0.7428 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8976 Z= 0.194 Angle : 0.525 7.138 12147 Z= 0.270 Chirality : 0.041 0.140 1352 Planarity : 0.004 0.042 1523 Dihedral : 7.184 59.604 1504 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.87 % Allowed : 11.71 % 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: -1.13 (0.23), residues: 1051 helix: 0.53 (0.24), residues: 424 sheet: -1.13 (0.31), residues: 220 loop : -1.83 (0.25), residues: 407 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 196 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 160 time to evaluate : 0.931 Fit side-chains outliers start: 36 outliers final: 12 residues processed: 177 average time/residue: 1.1712 time to fit residues: 221.5901 Evaluate side-chains 148 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 4 average time/residue: 0.4418 time to fit residues: 3.4682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 78 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 102 optimal weight: 0.0060 chunk 84 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- 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 U 33 ASN A 23 ASN A 59 GLN B 88 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 8976 Z= 0.317 Angle : 0.571 6.999 12147 Z= 0.299 Chirality : 0.044 0.152 1352 Planarity : 0.004 0.040 1523 Dihedral : 7.725 58.125 1504 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.62 % Allowed : 14.29 % Favored : 81.10 % 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: -0.75 (0.24), residues: 1051 helix: 0.80 (0.24), residues: 429 sheet: -0.99 (0.32), residues: 217 loop : -1.57 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.002 PHE B 234 TYR 0.015 0.002 TYR P 249 ARG 0.004 0.001 ARG N 38 *********************** 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 185 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 1.007 Fit side-chains outliers start: 43 outliers final: 26 residues processed: 162 average time/residue: 1.1081 time to fit residues: 192.6906 Evaluate side-chains 154 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 15 residues processed: 12 average time/residue: 0.2489 time to fit residues: 5.2085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 89 optimal weight: 0.0970 chunk 27 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8976 Z= 0.170 Angle : 0.480 8.075 12147 Z= 0.249 Chirality : 0.040 0.135 1352 Planarity : 0.003 0.036 1523 Dihedral : 7.061 57.443 1504 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.83 % Allowed : 15.90 % Favored : 79.27 % 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: -0.20 (0.25), residues: 1051 helix: 1.38 (0.25), residues: 421 sheet: -0.72 (0.32), residues: 208 loop : -1.35 (0.27), residues: 422 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 0.008 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 181 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 136 time to evaluate : 0.921 Fit side-chains outliers start: 45 outliers final: 22 residues processed: 163 average time/residue: 1.0181 time to fit residues: 179.7901 Evaluate side-chains 146 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 7 average time/residue: 0.1199 time to fit residues: 2.7112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8976 Z= 0.192 Angle : 0.494 8.261 12147 Z= 0.257 Chirality : 0.040 0.133 1352 Planarity : 0.003 0.036 1523 Dihedral : 6.928 55.203 1504 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.51 % Allowed : 17.08 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.25), residues: 1051 helix: 1.55 (0.25), residues: 422 sheet: -0.67 (0.32), residues: 209 loop : -1.22 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE P 256 TYR 0.013 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 177 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 135 time to evaluate : 1.049 Fit side-chains outliers start: 42 outliers final: 27 residues processed: 157 average time/residue: 1.0391 time to fit residues: 176.0910 Evaluate side-chains 158 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 17 residues processed: 11 average time/residue: 0.3745 time to fit residues: 6.3013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8976 Z= 0.153 Angle : 0.473 9.570 12147 Z= 0.246 Chirality : 0.039 0.133 1352 Planarity : 0.003 0.036 1523 Dihedral : 6.657 56.141 1504 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.76 % Allowed : 17.94 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1051 helix: 1.81 (0.25), residues: 418 sheet: -0.67 (0.32), residues: 216 loop : -1.03 (0.28), residues: 417 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 0.015 0.001 PHE P 256 TYR 0.012 0.001 TYR A 37 ARG 0.008 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 174 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 1.007 Fit side-chains outliers start: 35 outliers final: 22 residues processed: 162 average time/residue: 1.0790 time to fit residues: 188.3063 Evaluate side-chains 149 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 17 residues processed: 6 average time/residue: 0.5498 time to fit residues: 4.9454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 0.0000 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3873 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= 0.145 Angle : 0.479 9.062 12147 Z= 0.248 Chirality : 0.039 0.136 1352 Planarity : 0.003 0.036 1523 Dihedral : 6.521 59.443 1504 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.87 % Allowed : 19.12 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1051 helix: 1.85 (0.25), residues: 424 sheet: -0.51 (0.33), residues: 214 loop : -0.95 (0.28), residues: 413 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 0.015 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 170 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 0.898 Fit side-chains outliers start: 36 outliers final: 22 residues processed: 156 average time/residue: 1.0231 time to fit residues: 172.3678 Evaluate side-chains 148 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 7 average time/residue: 0.6103 time to fit residues: 6.2163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 50.0494 > 50: distance: 6 - 8: 9.957 distance: 8 - 9: 20.488 distance: 9 - 10: 13.917 distance: 10 - 11: 15.580 distance: 10 - 12: 8.397 distance: 12 - 13: 8.207 distance: 13 - 14: 15.355 distance: 13 - 16: 10.104 distance: 14 - 15: 12.134 distance: 14 - 20: 7.063 distance: 16 - 17: 15.637 distance: 17 - 18: 6.800 distance: 17 - 19: 4.619 distance: 20 - 21: 7.525 distance: 21 - 22: 25.864 distance: 21 - 24: 12.046 distance: 22 - 23: 18.164 distance: 22 - 27: 5.697 distance: 24 - 25: 17.144 distance: 24 - 26: 15.530 distance: 27 - 28: 3.666 distance: 28 - 31: 7.095 distance: 29 - 30: 3.817 distance: 29 - 36: 4.944 distance: 31 - 32: 17.533 distance: 32 - 33: 11.476 distance: 33 - 35: 12.404 distance: 36 - 37: 5.748 distance: 36 - 42: 10.805 distance: 37 - 38: 11.561 distance: 37 - 40: 21.196 distance: 38 - 39: 14.295 distance: 38 - 43: 3.247 distance: 40 - 41: 6.303 distance: 41 - 42: 11.852 distance: 43 - 44: 5.577 distance: 45 - 46: 4.531 distance: 45 - 47: 16.905 distance: 47 - 48: 7.449 distance: 48 - 49: 12.978 distance: 49 - 50: 10.052 distance: 49 - 51: 7.751 distance: 51 - 52: 8.180 distance: 52 - 53: 7.577 distance: 52 - 55: 3.974 distance: 53 - 57: 7.207 distance: 57 - 58: 8.028 distance: 57 - 106: 7.293 distance: 58 - 59: 5.268 distance: 58 - 61: 3.008 distance: 59 - 60: 8.711 distance: 59 - 65: 8.661 distance: 60 - 103: 9.229 distance: 61 - 62: 13.246 distance: 62 - 63: 3.138 distance: 62 - 64: 10.867 distance: 65 - 66: 10.174 distance: 66 - 67: 12.547 distance: 66 - 69: 12.770 distance: 67 - 68: 6.934 distance: 69 - 70: 10.723 distance: 70 - 71: 8.082 distance: 71 - 72: 7.515 distance: 72 - 73: 3.217 distance: 73 - 74: 3.608 distance: 73 - 75: 9.779