Starting phenix.real_space_refine on Thu Dec 7 21:06:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5g_33619/12_2023/7y5g_33619.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5g_33619/12_2023/7y5g_33619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5g_33619/12_2023/7y5g_33619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5g_33619/12_2023/7y5g_33619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5g_33619/12_2023/7y5g_33619.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5g_33619/12_2023/7y5g_33619.pdb" } resolution = 3.85 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= 0.125 sd= 0.202 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 Zn 6 6.06 5 S 30 5.16 5 C 3082 2.51 5 N 780 2.21 5 O 838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4736 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2365 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 2 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2365 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 2 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2381 SG CYS A 46 26.060 40.179 23.002 1.00 39.27 S ATOM 4684 SG CYS A 366 51.919 30.262 24.232 1.00 46.10 S ATOM 4709 SG CYS A 369 48.349 29.216 25.198 1.00 39.78 S ATOM 2319 SG CYS B 366 20.695 44.559 24.254 1.00 46.97 S ATOM 2344 SG CYS B 369 24.266 45.584 25.240 1.00 39.28 S ATOM 16 SG CYS B 46 46.540 34.628 23.002 1.00 38.21 S Time building chain proxies: 2.91, per 1000 atoms: 0.61 Number of scatterers: 4736 At special positions: 0 Unit cell: (73.7, 75.9, 104.5, 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) Zn 6 29.99 S 30 16.00 O 838 8.00 N 780 7.00 C 3082 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: 1.89 Conformation dependent library (CDL) restraints added in 836.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 45 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 47 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 366 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 369 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" ND1 HIS A 323 " pdb="ZN ZN A 402 " - pdb=" SG CYS B 46 " pdb="ZN ZN A 402 " - pdb=" NE2 HIS A 306 " pdb=" ZN A 403 " pdb="ZN ZN A 403 " - pdb=" NE2 HIS A 225 " pdb="ZN ZN A 403 " - pdb=" NE2 HIS A 100 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 323 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 46 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 306 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" NE2 HIS B 225 " pdb="ZN ZN B 402 " - pdb=" NE2 HIS B 100 " pdb=" ZN B 403 " pdb="ZN ZN B 403 " - pdb=" NE2 HIS B 45 " pdb="ZN ZN B 403 " - pdb=" ND1 HIS B 47 " pdb="ZN ZN B 403 " - pdb=" SG CYS A 366 " pdb="ZN ZN B 403 " - pdb=" SG CYS A 369 " Number of angles added : 2 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1156 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 66.6% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 86 removed outlier: 3.741A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 82 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.666A pdb=" N LEU B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 118 removed outlier: 3.956A pdb=" N ASP B 104 " --> pdb=" O HIS B 100 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 117 " --> pdb=" O CYS B 113 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 138 through 162 removed outlier: 3.966A pdb=" N VAL B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 191 removed outlier: 3.679A pdb=" N MET B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 246 removed outlier: 3.534A pdb=" N PHE B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 removed outlier: 4.509A pdb=" N ILE B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.730A pdb=" N THR B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.999A pdb=" N ASP B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 298 Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.957A pdb=" N ILE B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.726A pdb=" N CYS B 369 " --> pdb=" O CYS B 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 50 through 86 removed outlier: 3.745A pdb=" N ARG A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.673A pdb=" N LEU A 92 " --> pdb=" O ILE A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 118 removed outlier: 3.976A pdb=" N ASP A 104 " --> pdb=" O HIS A 100 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 138 through 162 removed outlier: 3.990A pdb=" N VAL A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 191 removed outlier: 3.699A pdb=" N MET A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 246 removed outlier: 3.542A pdb=" N PHE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.558A pdb=" N ILE A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.731A pdb=" N THR A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 removed outlier: 4.018A pdb=" N ASP A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 298 Processing helix chain 'A' and resid 331 through 345 removed outlier: 3.999A pdb=" N ILE A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.707A pdb=" N CYS A 369 " --> pdb=" O CYS A 366 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 309 through 314 removed outlier: 3.657A pdb=" N TRP B 311 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLN B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER B 351 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 302 through 304 removed outlier: 6.987A pdb=" N ALA A 325 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 314 removed outlier: 3.656A pdb=" N TRP A 311 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLN A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A 351 " --> pdb=" O VAL A 318 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 732 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: 1.12 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1468 1.34 - 1.46: 1037 1.46 - 1.58: 2281 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 4828 Sorted by residual: bond pdb=" N GLU A 281 " pdb=" CA GLU A 281 " ideal model delta sigma weight residual 1.461 1.470 -0.009 1.52e-02 4.33e+03 3.59e-01 bond pdb=" N GLU B 281 " pdb=" CA GLU B 281 " ideal model delta sigma weight residual 1.461 1.470 -0.009 1.52e-02 4.33e+03 3.58e-01 bond pdb=" N LYS B 246 " pdb=" CA LYS B 246 " ideal model delta sigma weight residual 1.462 1.456 0.005 9.30e-03 1.16e+04 3.30e-01 bond pdb=" CA LEU B 272 " pdb=" C LEU B 272 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.80e-02 3.09e+03 3.20e-01 bond pdb=" CA LEU A 272 " pdb=" C LEU A 272 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.80e-02 3.09e+03 3.19e-01 ... (remaining 4823 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.35: 134 107.35 - 114.01: 2934 114.01 - 120.68: 1981 120.68 - 127.34: 1457 127.34 - 134.01: 52 Bond angle restraints: 6558 Sorted by residual: angle pdb=" CA LEU A 275 " pdb=" CB LEU A 275 " pdb=" CG LEU A 275 " ideal model delta sigma weight residual 116.30 123.02 -6.72 3.50e+00 8.16e-02 3.68e+00 angle pdb=" CA LEU B 275 " pdb=" CB LEU B 275 " pdb=" CG LEU B 275 " ideal model delta sigma weight residual 116.30 123.01 -6.71 3.50e+00 8.16e-02 3.68e+00 angle pdb=" CA LEU B 272 " pdb=" C LEU B 272 " pdb=" O LEU B 272 " ideal model delta sigma weight residual 119.23 122.14 -2.91 1.54e+00 4.22e-01 3.57e+00 angle pdb=" C MET B 280 " pdb=" N GLU B 281 " pdb=" CA GLU B 281 " ideal model delta sigma weight residual 122.07 124.76 -2.69 1.43e+00 4.89e-01 3.54e+00 angle pdb=" CA LEU A 272 " pdb=" C LEU A 272 " pdb=" O LEU A 272 " ideal model delta sigma weight residual 119.23 122.12 -2.89 1.54e+00 4.22e-01 3.53e+00 ... (remaining 6553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 2554 15.89 - 31.77: 248 31.77 - 47.66: 52 47.66 - 63.55: 0 63.55 - 79.43: 4 Dihedral angle restraints: 2858 sinusoidal: 1086 harmonic: 1772 Sorted by residual: dihedral pdb=" CA THR A 124 " pdb=" C THR A 124 " pdb=" N ARG A 125 " pdb=" CA ARG A 125 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.91e+00 dihedral pdb=" CA THR B 124 " pdb=" C THR B 124 " pdb=" N ARG B 125 " pdb=" CA ARG B 125 " ideal model delta harmonic sigma weight residual 180.00 164.28 15.72 0 5.00e+00 4.00e-02 9.88e+00 dihedral pdb=" CA ARG B 273 " pdb=" CB ARG B 273 " pdb=" CG ARG B 273 " pdb=" CD ARG B 273 " ideal model delta sinusoidal sigma weight residual -60.00 -107.12 47.12 3 1.50e+01 4.44e-03 8.44e+00 ... (remaining 2855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 408 0.024 - 0.048: 255 0.048 - 0.072: 104 0.072 - 0.096: 29 0.096 - 0.120: 8 Chirality restraints: 804 Sorted by residual: chirality pdb=" CA ILE B 319 " pdb=" N ILE B 319 " pdb=" C ILE B 319 " pdb=" CB ILE B 319 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA ILE A 319 " pdb=" N ILE A 319 " pdb=" C ILE A 319 " pdb=" CB ILE A 319 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.34e-01 chirality pdb=" CA ILE B 354 " pdb=" N ILE B 354 " pdb=" C ILE B 354 " pdb=" CB ILE B 354 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.92e-01 ... (remaining 801 not shown) Planarity restraints: 794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 363 " -0.011 5.00e-02 4.00e+02 1.73e-02 4.77e-01 pdb=" N PRO A 364 " 0.030 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 281 " -0.003 2.00e-02 2.50e+03 5.81e-03 3.37e-01 pdb=" C GLU A 281 " 0.010 2.00e-02 2.50e+03 pdb=" O GLU A 281 " -0.004 2.00e-02 2.50e+03 pdb=" N GLY A 282 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 281 " 0.003 2.00e-02 2.50e+03 5.72e-03 3.27e-01 pdb=" C GLU B 281 " -0.010 2.00e-02 2.50e+03 pdb=" O GLU B 281 " 0.004 2.00e-02 2.50e+03 pdb=" N GLY B 282 " 0.003 2.00e-02 2.50e+03 ... (remaining 791 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 38 2.65 - 3.21: 4355 3.21 - 3.77: 6467 3.77 - 4.34: 8300 4.34 - 4.90: 13548 Nonbonded interactions: 32708 Sorted by model distance: nonbonded pdb=" OE2 GLU B 357 " pdb="ZN ZN B 401 " model vdw 2.084 2.230 nonbonded pdb=" OE2 GLU A 357 " pdb="ZN ZN A 402 " model vdw 2.087 2.230 nonbonded pdb=" OG SER B 239 " pdb=" OD1 ASP B 253 " model vdw 2.195 2.440 nonbonded pdb=" OD1 ASP A 229 " pdb="ZN ZN A 403 " model vdw 2.356 2.230 nonbonded pdb=" OE1 GLU A 357 " pdb="ZN ZN A 402 " model vdw 2.371 2.230 ... (remaining 32703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.430 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: 0.000 Extract box with map and model: 1.690 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.440 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 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 : 0.002 0.017 4828 Z= 0.130 Angle : 0.433 6.719 6558 Z= 0.215 Chirality : 0.036 0.120 804 Planarity : 0.002 0.017 794 Dihedral : 12.736 79.432 1702 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.34), residues: 592 helix: 0.34 (0.26), residues: 382 sheet: -1.47 (0.50), residues: 50 loop : -0.07 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 311 HIS 0.002 0.001 HIS A 309 PHE 0.004 0.000 PHE B 63 TYR 0.004 0.000 TYR B 289 ARG 0.003 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.548 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1778 time to fit residues: 18.6318 Evaluate side-chains 48 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.503 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0270 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4828 Z= 0.281 Angle : 0.578 6.674 6558 Z= 0.311 Chirality : 0.040 0.135 804 Planarity : 0.004 0.035 794 Dihedral : 4.129 17.528 638 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.26 % Allowed : 12.45 % Favored : 85.28 % 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: 0.61 (0.36), residues: 592 helix: 1.20 (0.28), residues: 382 sheet: -1.81 (0.50), residues: 50 loop : -0.62 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 311 HIS 0.004 0.001 HIS A 309 PHE 0.018 0.002 PHE A 76 TYR 0.019 0.002 TYR B 154 ARG 0.005 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.535 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.1306 time to fit residues: 10.3695 Evaluate side-chains 55 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.456 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0430 time to fit residues: 1.3637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4828 Z= 0.372 Angle : 0.615 7.787 6558 Z= 0.324 Chirality : 0.041 0.122 804 Planarity : 0.004 0.030 794 Dihedral : 4.730 18.268 638 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.26 % Allowed : 16.04 % Favored : 81.70 % 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: 0.45 (0.36), residues: 592 helix: 1.15 (0.28), residues: 372 sheet: -1.91 (0.51), residues: 48 loop : -0.75 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 130 HIS 0.006 0.002 HIS A 309 PHE 0.018 0.002 PHE A 76 TYR 0.017 0.001 TYR A 154 ARG 0.006 0.001 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.563 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 60 average time/residue: 0.1725 time to fit residues: 13.4633 Evaluate side-chains 53 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0464 time to fit residues: 1.3986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 40.0000 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 26 optimal weight: 7.9990 chunk 36 optimal weight: 0.0170 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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: 0.7021 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4828 Z= 0.122 Angle : 0.445 5.708 6558 Z= 0.236 Chirality : 0.036 0.131 804 Planarity : 0.003 0.025 794 Dihedral : 3.713 15.873 638 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.13 % Allowed : 18.49 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.36), residues: 592 helix: 1.62 (0.28), residues: 372 sheet: -1.65 (0.55), residues: 50 loop : -0.80 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 311 HIS 0.001 0.000 HIS A 288 PHE 0.018 0.001 PHE B 76 TYR 0.016 0.001 TYR A 154 ARG 0.010 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.547 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 0.1753 time to fit residues: 12.2532 Evaluate side-chains 46 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.559 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0475 time to fit residues: 0.9228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 0.0670 chunk 11 optimal weight: 40.0000 chunk 34 optimal weight: 50.0000 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4828 Z= 0.311 Angle : 0.557 6.877 6558 Z= 0.292 Chirality : 0.040 0.119 804 Planarity : 0.003 0.020 794 Dihedral : 4.436 17.473 638 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.58 % Allowed : 16.23 % Favored : 80.19 % 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: 0.79 (0.36), residues: 592 helix: 1.48 (0.28), residues: 372 sheet: -1.81 (0.57), residues: 50 loop : -0.78 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 130 HIS 0.005 0.001 HIS A 309 PHE 0.019 0.002 PHE B 76 TYR 0.017 0.001 TYR B 154 ARG 0.006 0.001 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 0.563 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 64 average time/residue: 0.1444 time to fit residues: 12.6163 Evaluate side-chains 54 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0567 time to fit residues: 1.6830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.0870 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4828 Z= 0.137 Angle : 0.465 7.207 6558 Z= 0.241 Chirality : 0.036 0.127 804 Planarity : 0.002 0.019 794 Dihedral : 3.932 16.434 638 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.70 % Allowed : 18.11 % Favored : 80.19 % 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: 1.04 (0.36), residues: 592 helix: 1.75 (0.28), residues: 372 sheet: -1.58 (0.62), residues: 50 loop : -0.92 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 311 HIS 0.002 0.000 HIS A 309 PHE 0.021 0.001 PHE B 76 TYR 0.019 0.001 TYR A 154 ARG 0.004 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.541 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 53 average time/residue: 0.1532 time to fit residues: 11.0359 Evaluate side-chains 46 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0469 time to fit residues: 1.1095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 30.0000 chunk 17 optimal weight: 30.0000 chunk 11 optimal weight: 40.0000 chunk 39 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4828 Z= 0.204 Angle : 0.519 9.942 6558 Z= 0.266 Chirality : 0.038 0.118 804 Planarity : 0.002 0.016 794 Dihedral : 4.132 17.069 638 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.94 % Allowed : 20.00 % Favored : 79.06 % 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: 0.89 (0.36), residues: 592 helix: 1.68 (0.28), residues: 372 sheet: -1.87 (0.58), residues: 50 loop : -1.02 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 311 HIS 0.003 0.001 HIS A 309 PHE 0.012 0.001 PHE B 63 TYR 0.021 0.001 TYR B 249 ARG 0.003 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.699 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 46 average time/residue: 0.1590 time to fit residues: 10.0683 Evaluate side-chains 43 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.522 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0466 time to fit residues: 0.9038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.0010 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 53 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 overall best weight: 0.9128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN B 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4828 Z= 0.127 Angle : 0.467 9.245 6558 Z= 0.240 Chirality : 0.036 0.124 804 Planarity : 0.002 0.015 794 Dihedral : 3.799 16.806 638 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.38 % Allowed : 20.57 % Favored : 79.06 % 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: 1.11 (0.36), residues: 592 helix: 1.87 (0.28), residues: 372 sheet: -1.76 (0.59), residues: 50 loop : -0.99 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 311 HIS 0.001 0.000 HIS A 309 PHE 0.020 0.001 PHE A 76 TYR 0.020 0.001 TYR B 249 ARG 0.003 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.574 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 0.1587 time to fit residues: 9.1139 Evaluate side-chains 41 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0551 time to fit residues: 0.9115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 ASN A 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4828 Z= 0.121 Angle : 0.469 8.598 6558 Z= 0.239 Chirality : 0.036 0.126 804 Planarity : 0.002 0.015 794 Dihedral : 3.685 17.022 638 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 22.26 % Favored : 77.74 % 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: 1.34 (0.37), residues: 592 helix: 1.94 (0.28), residues: 372 sheet: -1.66 (0.60), residues: 50 loop : -0.61 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 311 HIS 0.001 0.000 HIS B 309 PHE 0.011 0.001 PHE A 78 TYR 0.020 0.001 TYR A 154 ARG 0.003 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.562 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1635 time to fit residues: 9.3528 Evaluate side-chains 39 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.549 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 37 optimal weight: 0.0040 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.0170 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 0.0010 chunk 13 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 0.0870 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 4828 Z= 0.099 Angle : 0.441 8.453 6558 Z= 0.223 Chirality : 0.035 0.131 804 Planarity : 0.002 0.015 794 Dihedral : 3.413 17.447 638 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.57 % Allowed : 21.89 % Favored : 77.55 % 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: 1.51 (0.37), residues: 592 helix: 2.04 (0.29), residues: 372 sheet: -1.52 (0.62), residues: 50 loop : -0.49 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 311 HIS 0.001 0.000 HIS B 225 PHE 0.022 0.001 PHE A 76 TYR 0.020 0.001 TYR A 154 ARG 0.003 0.000 ARG A 159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.522 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.2150 time to fit residues: 12.6499 Evaluate side-chains 43 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.512 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0452 time to fit residues: 0.9986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 54 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.231542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.212566 restraints weight = 61163.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.214634 restraints weight = 39045.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.214389 restraints weight = 32263.444| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4828 Z= 0.146 Angle : 0.483 7.966 6558 Z= 0.245 Chirality : 0.037 0.125 804 Planarity : 0.002 0.022 794 Dihedral : 3.631 17.545 638 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.38 % Allowed : 23.02 % Favored : 76.60 % 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: 1.53 (0.37), residues: 592 helix: 2.04 (0.28), residues: 372 sheet: -1.56 (0.60), residues: 50 loop : -0.42 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 311 HIS 0.002 0.001 HIS A 309 PHE 0.010 0.001 PHE B 63 TYR 0.021 0.001 TYR B 154 ARG 0.010 0.001 ARG A 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1141.46 seconds wall clock time: 21 minutes 23.10 seconds (1283.10 seconds total)