Starting phenix.real_space_refine on Fri Nov 17 10:59:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g2x_3331/11_2023/5g2x_3331.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g2x_3331/11_2023/5g2x_3331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g2x_3331/11_2023/5g2x_3331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g2x_3331/11_2023/5g2x_3331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g2x_3331/11_2023/5g2x_3331.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g2x_3331/11_2023/5g2x_3331.pdb" } resolution = 3.8 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= 0.001 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: 5 Type Number sf(0) Gaussians P 703 5.49 5 S 19 5.16 5 C 9320 2.51 5 N 3467 2.21 5 O 5563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 19072 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 14825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 14825 Classifications: {'RNA': 692} Modifications used: {'5*END': 1, 'rna2p_pur': 64, 'rna2p_pyr': 34, 'rna3p_pur': 345, 'rna3p_pyr': 249} Link IDs: {'rna2p': 97, 'rna3p': 594} Chain breaks: 3 Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'RNA': 12} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "C" Number of atoms: 3997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3997 Classifications: {'peptide': 487} Link IDs: {'CIS': 24, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 447} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 10.70, per 1000 atoms: 0.56 Number of scatterers: 19072 At special positions: 0 Unit cell: (156.785, 152.865, 139.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 703 15.00 O 5563 8.00 N 3467 7.00 C 9320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 8.93 Conformation dependent library (CDL) restraints added in 833.4 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 36.6% alpha, 0.0% beta 42 base pairs and 325 stacking pairs defined. Time for finding SS restraints: 6.71 Creating SS restraints... Processing helix chain 'C' and resid 5 through 13 removed outlier: 4.153A pdb=" N GLU C 9 " --> pdb=" O MET C 5 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 11 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 12 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 5 through 13' Processing helix chain 'C' and resid 30 through 41 removed outlier: 4.746A pdb=" N ASP C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 38 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR C 40 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLN C 41 " --> pdb=" O TYR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.559A pdb=" N GLN C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 68 through 73' Processing helix chain 'C' and resid 106 through 121 removed outlier: 3.807A pdb=" N ILE C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE C 116 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 148 removed outlier: 4.273A pdb=" N LYS C 144 " --> pdb=" O HIS C 140 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 140 through 148' Processing helix chain 'C' and resid 171 through 179 removed outlier: 4.416A pdb=" N ILE C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU C 179 " --> pdb=" O GLY C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 197 removed outlier: 7.577A pdb=" N TYR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS C 195 " --> pdb=" O TYR C 191 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ALA C 196 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLY C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 197' Processing helix chain 'C' and resid 217 through 248 removed outlier: 3.815A pdb=" N ASN C 223 " --> pdb=" O PRO C 219 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS C 231 " --> pdb=" O HIS C 227 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN C 235 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU C 236 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS C 239 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ARG C 242 " --> pdb=" O MET C 238 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER C 244 " --> pdb=" O PHE C 240 " (cutoff:3.500A) Proline residue: C 245 - end of helix removed outlier: 4.466A pdb=" N ILE C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 331 removed outlier: 3.874A pdb=" N GLN C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TRP C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS C 325 " --> pdb=" O CYS C 321 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS C 329 " --> pdb=" O LYS C 325 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 343 No H-bonds generated for 'chain 'C' and resid 341 through 343' Processing helix chain 'C' and resid 393 through 400 removed outlier: 4.603A pdb=" N PHE C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE C 398 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N PHE C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 440 removed outlier: 3.952A pdb=" N ILE C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR C 432 " --> pdb=" O ILE C 428 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG C 437 " --> pdb=" O ASN C 433 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY C 438 " --> pdb=" O SER C 434 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 470 removed outlier: 3.550A pdb=" N ALA C 456 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR C 457 " --> pdb=" O ASN C 453 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU C 458 " --> pdb=" O TYR C 454 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET C 459 " --> pdb=" O PHE C 455 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR C 461 " --> pdb=" O TYR C 457 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C 464 " --> pdb=" O GLU C 460 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 470 " --> pdb=" O THR C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 538 removed outlier: 4.339A pdb=" N THR C 533 " --> pdb=" O TYR C 529 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 535 " --> pdb=" O ARG C 531 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG C 537 " --> pdb=" O THR C 533 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 553 No H-bonds generated for 'chain 'C' and resid 552 through 553' 31 hydrogen bonds defined for protein. 93 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 325 stacking parallelities Total time for adding SS restraints: 7.55 Time building geometry restraints manager: 9.62 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: 3171 1.34 - 1.45: 9106 1.45 - 1.57: 7265 1.57 - 1.69: 1402 1.69 - 1.81: 28 Bond restraints: 20972 Sorted by residual: bond pdb=" C HIS C 591 " pdb=" N ARG C 592 " ideal model delta sigma weight residual 1.329 1.231 0.098 1.40e-02 5.10e+03 4.87e+01 bond pdb=" CA ASN C 18 " pdb=" C ASN C 18 " ideal model delta sigma weight residual 1.523 1.554 -0.031 1.34e-02 5.57e+03 5.28e+00 bond pdb=" CA TYR C 527 " pdb=" C TYR C 527 " ideal model delta sigma weight residual 1.520 1.551 -0.032 1.40e-02 5.10e+03 5.15e+00 bond pdb=" CA TYR C 44 " pdb=" C TYR C 44 " ideal model delta sigma weight residual 1.524 1.547 -0.024 1.26e-02 6.30e+03 3.53e+00 bond pdb=" CA ASN C 46 " pdb=" C ASN C 46 " ideal model delta sigma weight residual 1.524 1.546 -0.023 1.26e-02 6.30e+03 3.23e+00 ... (remaining 20967 not shown) Histogram of bond angle deviations from ideal: 100.84 - 107.47: 4282 107.47 - 114.10: 13311 114.10 - 120.73: 7413 120.73 - 127.36: 5333 127.36 - 133.98: 1465 Bond angle restraints: 31804 Sorted by residual: angle pdb=" C ASN C 18 " pdb=" N ILE C 19 " pdb=" CA ILE C 19 " ideal model delta sigma weight residual 121.70 132.69 -10.99 1.80e+00 3.09e-01 3.73e+01 angle pdb=" CA ASN C 18 " pdb=" C ASN C 18 " pdb=" N ILE C 19 " ideal model delta sigma weight residual 116.84 124.40 -7.56 1.71e+00 3.42e-01 1.95e+01 angle pdb=" C VAL C 375 " pdb=" N LYS C 376 " pdb=" CA LYS C 376 " ideal model delta sigma weight residual 121.70 129.32 -7.62 1.80e+00 3.09e-01 1.79e+01 angle pdb=" C LEU C 100 " pdb=" CA LEU C 100 " pdb=" CB LEU C 100 " ideal model delta sigma weight residual 116.54 110.38 6.16 1.46e+00 4.69e-01 1.78e+01 angle pdb=" CA GLY C 48 " pdb=" C GLY C 48 " pdb=" O GLY C 48 " ideal model delta sigma weight residual 122.76 118.42 4.34 1.12e+00 7.97e-01 1.50e+01 ... (remaining 31799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 10688 35.59 - 71.19: 188 71.19 - 106.78: 22 106.78 - 142.37: 3 142.37 - 177.96: 8 Dihedral angle restraints: 10909 sinusoidal: 9481 harmonic: 1428 Sorted by residual: dihedral pdb=" O4' C A 316 " pdb=" C1' C A 316 " pdb=" N1 C A 316 " pdb=" C2 C A 316 " ideal model delta sinusoidal sigma weight residual -128.00 49.96 -177.96 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C A 487 " pdb=" C1' C A 487 " pdb=" N1 C A 487 " pdb=" C2 C A 487 " ideal model delta sinusoidal sigma weight residual -128.00 48.87 -176.87 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C4' U A 177 " pdb=" C3' U A 177 " pdb=" O3' U A 177 " pdb=" P A A 178 " ideal model delta sinusoidal sigma weight residual -110.00 63.48 -173.48 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 10906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3898 0.036 - 0.073: 155 0.073 - 0.109: 43 0.109 - 0.146: 10 0.146 - 0.182: 8 Chirality restraints: 4114 Sorted by residual: chirality pdb=" C3' A A 149 " pdb=" C4' A A 149 " pdb=" O3' A A 149 " pdb=" C2' A A 149 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" C3' C B 1 " pdb=" C4' C B 1 " pdb=" O3' C B 1 " pdb=" C2' C B 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.66 0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" C3' G A 559 " pdb=" C4' G A 559 " pdb=" O3' G A 559 " pdb=" C2' G A 559 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 4111 not shown) Planarity restraints: 1389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 123 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO C 124 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 218 " -0.014 5.00e-02 4.00e+02 2.12e-02 7.21e-01 pdb=" N PRO C 219 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO C 219 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 219 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 211 " -0.013 5.00e-02 4.00e+02 1.96e-02 6.16e-01 pdb=" N PRO C 212 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " -0.011 5.00e-02 4.00e+02 ... (remaining 1386 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2529 2.76 - 3.29: 15686 3.29 - 3.83: 33394 3.83 - 4.36: 40872 4.36 - 4.90: 54857 Nonbonded interactions: 147338 Sorted by model distance: nonbonded pdb=" O2' C B 1 " pdb=" O4' A B 2 " model vdw 2.219 2.440 nonbonded pdb=" O2' C A2395 " pdb=" O5' A A2396 " model vdw 2.278 2.440 nonbonded pdb=" O2' C A 7 " pdb=" O2' A A 516 " model vdw 2.289 2.440 nonbonded pdb=" O ARG C 25 " pdb=" OH TYR C 29 " model vdw 2.290 2.440 nonbonded pdb=" OP2 A A 563 " pdb=" OH TYR C 36 " model vdw 2.295 2.440 ... (remaining 147333 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 group one per residue 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: 0.560 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: 0.020 Extract box with map and model: 2.770 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 53.890 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2869 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 : 0.001 0.098 20972 Z= 0.090 Angle : 0.321 10.992 31804 Z= 0.186 Chirality : 0.018 0.182 4114 Planarity : 0.002 0.046 1389 Dihedral : 11.564 177.965 9991 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 5.88 % Allowed : 19.75 % Favored : 74.37 % Rotamer: Outliers : 0.45 % Allowed : 1.59 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % 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: -5.72 (0.28), residues: 476 helix: -4.59 (0.17), residues: 102 sheet: -4.08 (1.23), residues: 9 loop : -3.91 (0.26), residues: 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.3741 time to fit residues: 66.3616 Evaluate side-chains 65 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1611 time to fit residues: 1.1805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 ASN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 GLN C 223 ASN C 381 ASN ** C 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3795 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 20972 Z= 0.316 Angle : 0.920 13.026 31804 Z= 0.452 Chirality : 0.042 0.245 4114 Planarity : 0.006 0.048 1389 Dihedral : 14.559 176.634 8969 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 26.75 Ramachandran Plot: Outliers : 1.05 % Allowed : 17.02 % Favored : 81.93 % Rotamer: Outliers : 4.54 % Allowed : 9.52 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % 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: -5.06 (0.30), residues: 476 helix: -2.83 (0.35), residues: 118 sheet: None (None), residues: 0 loop : -3.91 (0.27), residues: 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 90 average time/residue: 0.3154 time to fit residues: 43.5499 Evaluate side-chains 60 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1671 time to fit residues: 3.7333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 0.2980 chunk 36 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN ** C 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3830 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 20972 Z= 0.186 Angle : 0.602 12.049 31804 Z= 0.305 Chirality : 0.031 0.192 4114 Planarity : 0.004 0.044 1389 Dihedral : 14.808 175.882 8969 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 1.05 % Allowed : 17.23 % Favored : 81.72 % Rotamer: Outliers : 2.72 % Allowed : 14.74 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % 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: -4.44 (0.33), residues: 476 helix: -1.72 (0.48), residues: 109 sheet: None (None), residues: 0 loop : -3.70 (0.27), residues: 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 65 average time/residue: 0.2678 time to fit residues: 28.5158 Evaluate side-chains 45 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1637 time to fit residues: 2.0892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 102 optimal weight: 0.0980 chunk 30 optimal weight: 20.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3843 moved from start: 0.6255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20972 Z= 0.145 Angle : 0.564 11.992 31804 Z= 0.287 Chirality : 0.029 0.184 4114 Planarity : 0.004 0.045 1389 Dihedral : 14.950 177.969 8969 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 1.05 % Allowed : 15.34 % Favored : 83.61 % Rotamer: Outliers : 2.95 % Allowed : 16.33 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % 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: -4.26 (0.33), residues: 476 helix: -1.51 (0.47), residues: 115 sheet: None (None), residues: 0 loop : -3.62 (0.27), residues: 361 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 61 average time/residue: 0.2818 time to fit residues: 27.7325 Evaluate side-chains 52 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1589 time to fit residues: 3.2484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 84 optimal weight: 0.0050 chunk 47 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 102 optimal weight: 0.0270 chunk 28 optimal weight: 20.0000 overall best weight: 2.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN ** C 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN C 536 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4129 moved from start: 0.8288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 20972 Z= 0.220 Angle : 0.709 12.051 31804 Z= 0.358 Chirality : 0.035 0.205 4114 Planarity : 0.005 0.053 1389 Dihedral : 16.563 175.749 8969 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 27.27 Ramachandran Plot: Outliers : 1.05 % Allowed : 17.86 % Favored : 81.09 % Rotamer: Outliers : 2.72 % Allowed : 16.33 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % 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: -4.59 (0.32), residues: 476 helix: -1.61 (0.46), residues: 126 sheet: None (None), residues: 0 loop : -3.97 (0.26), residues: 350 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 60 average time/residue: 0.3154 time to fit residues: 30.1602 Evaluate side-chains 51 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1881 time to fit residues: 3.3632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 66 optimal weight: 50.0000 chunk 28 optimal weight: 20.0000 chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 433 ASN C 450 ASN C 451 GLN C 536 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4329 moved from start: 0.9953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20972 Z= 0.301 Angle : 0.817 12.289 31804 Z= 0.412 Chirality : 0.041 0.261 4114 Planarity : 0.006 0.059 1389 Dihedral : 17.993 176.106 8969 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 34.82 Ramachandran Plot: Outliers : 1.05 % Allowed : 15.97 % Favored : 82.98 % Rotamer: Outliers : 2.72 % Allowed : 18.37 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % 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: -4.91 (0.31), residues: 476 helix: -2.11 (0.42), residues: 128 sheet: None (None), residues: 0 loop : -4.08 (0.26), residues: 348 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 73 average time/residue: 0.3090 time to fit residues: 35.3642 Evaluate side-chains 57 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1744 time to fit residues: 2.4628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 65 optimal weight: 50.0000 chunk 83 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 71 optimal weight: 0.3980 chunk 69 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4378 moved from start: 1.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20972 Z= 0.285 Angle : 0.792 12.132 31804 Z= 0.398 Chirality : 0.040 0.316 4114 Planarity : 0.006 0.059 1389 Dihedral : 18.489 174.962 8969 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 33.82 Ramachandran Plot: Outliers : 1.26 % Allowed : 18.07 % Favored : 80.67 % Rotamer: Outliers : 2.49 % Allowed : 18.59 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % 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: -4.93 (0.31), residues: 476 helix: -1.99 (0.42), residues: 132 sheet: None (None), residues: 0 loop : -4.18 (0.26), residues: 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 66 average time/residue: 0.2860 time to fit residues: 30.1513 Evaluate side-chains 54 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1621 time to fit residues: 2.7321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4516 moved from start: 1.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20972 Z= 0.358 Angle : 0.925 12.215 31804 Z= 0.465 Chirality : 0.046 0.279 4114 Planarity : 0.007 0.065 1389 Dihedral : 19.399 175.374 8969 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 41.82 Ramachandran Plot: Outliers : 1.05 % Allowed : 18.49 % Favored : 80.46 % Rotamer: Outliers : 1.81 % Allowed : 20.63 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % 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: -5.11 (0.29), residues: 476 helix: -2.18 (0.39), residues: 133 sheet: None (None), residues: 0 loop : -4.29 (0.25), residues: 343 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 63 average time/residue: 0.3467 time to fit residues: 32.9852 Evaluate side-chains 54 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3543 time to fit residues: 2.3594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 63 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 112 optimal weight: 0.0370 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4134 moved from start: 1.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20972 Z= 0.148 Angle : 0.641 12.124 31804 Z= 0.326 Chirality : 0.033 0.192 4114 Planarity : 0.005 0.042 1389 Dihedral : 18.171 178.319 8969 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 1.05 % Allowed : 15.97 % Favored : 82.98 % Rotamer: Outliers : 1.36 % Allowed : 20.86 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.62 (0.32), residues: 476 helix: -1.44 (0.46), residues: 123 sheet: None (None), residues: 0 loop : -4.05 (0.25), residues: 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 64 average time/residue: 0.3352 time to fit residues: 32.7312 Evaluate side-chains 51 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1712 time to fit residues: 1.1654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 77 optimal weight: 0.0070 chunk 117 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 99 optimal weight: 0.0010 overall best weight: 4.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4417 moved from start: 1.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20972 Z= 0.280 Angle : 0.795 12.027 31804 Z= 0.398 Chirality : 0.039 0.224 4114 Planarity : 0.005 0.051 1389 Dihedral : 18.823 179.961 8969 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 34.30 Ramachandran Plot: Outliers : 1.26 % Allowed : 18.28 % Favored : 80.46 % Rotamer: Outliers : 0.23 % Allowed : 21.09 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % 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: -4.77 (0.31), residues: 476 helix: -1.90 (0.43), residues: 127 sheet: None (None), residues: 0 loop : -4.04 (0.26), residues: 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.833 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.3442 time to fit residues: 27.4795 Evaluate side-chains 48 residues out of total 442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 20.0000 chunk 86 optimal weight: 0.0040 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 82 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 overall best weight: 5.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 167 ASN ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.113512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.091920 restraints weight = 107443.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.093375 restraints weight = 56965.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.093958 restraints weight = 36994.152| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 1.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 20972 Z= 0.346 Angle : 0.905 12.538 31804 Z= 0.454 Chirality : 0.045 0.279 4114 Planarity : 0.007 0.136 1389 Dihedral : 19.768 179.849 8969 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 41.01 Ramachandran Plot: Outliers : 1.26 % Allowed : 20.59 % Favored : 78.15 % Rotamer: Outliers : 0.68 % Allowed : 22.45 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.93 (0.31), residues: 476 helix: -2.28 (0.39), residues: 132 sheet: None (None), residues: 0 loop : -4.04 (0.27), residues: 344 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2260.01 seconds wall clock time: 43 minutes 34.82 seconds (2614.82 seconds total)