Starting phenix.real_space_refine on Tue Jul 29 07:53:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6of2_20040/07_2025/6of2_20040.cif Found real_map, /net/cci-nas-00/data/ceres_data/6of2_20040/07_2025/6of2_20040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6of2_20040/07_2025/6of2_20040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6of2_20040/07_2025/6of2_20040.map" model { file = "/net/cci-nas-00/data/ceres_data/6of2_20040/07_2025/6of2_20040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6of2_20040/07_2025/6of2_20040.cif" } resolution = 2.9 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= 0.005 sd= 0.705 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 7048 2.51 5 N 1930 2.21 5 O 2020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11062 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1451 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4048 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 52, 'TRANS': 475} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: E, D Time building chain proxies: 8.91, per 1000 atoms: 0.81 Number of scatterers: 11062 At special positions: 0 Unit cell: (145.8, 87.48, 90.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 6 15.00 Mg 2 11.99 O 2020 8.00 N 1930 7.00 C 7048 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.8 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 40.1% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 4.074A pdb=" N LEU A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 93 through 115 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 134 through 147 removed outlier: 4.064A pdb=" N VAL A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 Processing helix chain 'A' and resid 171 through 175 removed outlier: 4.164A pdb=" N GLY A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 203 removed outlier: 3.637A pdb=" N LEU B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 211 removed outlier: 3.561A pdb=" N ASN B 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 242 through 257 removed outlier: 3.603A pdb=" N ASN B 246 " --> pdb=" O HIS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 367 through 387 Processing helix chain 'B' and resid 403 through 417 Processing helix chain 'B' and resid 429 through 443 removed outlier: 3.642A pdb=" N SER B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 Processing helix chain 'B' and resid 535 through 544 removed outlier: 4.160A pdb=" N SER B 540 " --> pdb=" O PRO B 536 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.506A pdb=" N SER B 660 " --> pdb=" O SER B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 691 removed outlier: 4.340A pdb=" N TYR B 680 " --> pdb=" O PRO B 676 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 684 " --> pdb=" O TYR B 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 4.074A pdb=" N LEU D 15 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 41 through 64 Processing helix chain 'D' and resid 67 through 84 Processing helix chain 'D' and resid 93 through 115 Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 134 through 147 removed outlier: 4.062A pdb=" N VAL D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 170 Processing helix chain 'D' and resid 171 through 175 removed outlier: 4.165A pdb=" N GLY D 175 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 203 removed outlier: 3.636A pdb=" N LEU E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 203 " --> pdb=" O GLY E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 211 removed outlier: 3.560A pdb=" N ASN E 207 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Proline residue: E 208 - end of helix Processing helix chain 'E' and resid 242 through 257 removed outlier: 3.603A pdb=" N ASN E 246 " --> pdb=" O HIS E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 330 through 334 Processing helix chain 'E' and resid 367 through 387 Processing helix chain 'E' and resid 403 through 417 Processing helix chain 'E' and resid 429 through 443 removed outlier: 3.642A pdb=" N SER E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 484 Processing helix chain 'E' and resid 535 through 544 removed outlier: 4.160A pdb=" N SER E 540 " --> pdb=" O PRO E 536 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP E 541 " --> pdb=" O GLU E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 660 removed outlier: 3.507A pdb=" N SER E 660 " --> pdb=" O SER E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 691 removed outlier: 4.341A pdb=" N TYR E 680 " --> pdb=" O PRO E 676 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL E 681 " --> pdb=" O THR E 677 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY E 683 " --> pdb=" O ALA E 679 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU E 684 " --> pdb=" O TYR E 680 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 349 removed outlier: 7.530A pdb=" N GLU B 646 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N VAL B 638 " --> pdb=" O GLU B 646 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS B 648 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU B 550 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B 632 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET B 548 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 122 through 125 removed outlier: 6.503A pdb=" N VAL B 188 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 190 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 143 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 125 removed outlier: 6.503A pdb=" N VAL B 188 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 190 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 137 through 139 Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 358 removed outlier: 6.812A pdb=" N LEU B 320 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N MET B 356 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 318 " --> pdb=" O MET B 356 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET B 301 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASN B 396 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU B 303 " --> pdb=" O ASN B 396 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 264 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 263 " --> pdb=" O GLU B 420 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU B 422 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE B 265 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'D' and resid 347 through 349 removed outlier: 7.530A pdb=" N GLU E 646 " --> pdb=" O VAL E 638 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VAL E 638 " --> pdb=" O GLU E 646 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS E 648 " --> pdb=" O ARG E 636 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU E 550 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU E 632 " --> pdb=" O MET E 548 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET E 548 " --> pdb=" O LEU E 632 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 122 through 125 removed outlier: 6.503A pdb=" N VAL E 188 " --> pdb=" O HIS E 150 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU E 190 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY E 143 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 122 through 125 removed outlier: 6.503A pdb=" N VAL E 188 " --> pdb=" O HIS E 150 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU E 190 " --> pdb=" O LYS E 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 137 through 139 Processing sheet with id=AB3, first strand: chain 'E' and resid 351 through 358 removed outlier: 6.812A pdb=" N LEU E 320 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET E 356 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL E 318 " --> pdb=" O MET E 356 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET E 301 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASN E 396 " --> pdb=" O MET E 301 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU E 303 " --> pdb=" O ASN E 396 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU E 264 " --> pdb=" O VAL E 395 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE E 263 " --> pdb=" O GLU E 420 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU E 422 " --> pdb=" O ILE E 263 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE E 265 " --> pdb=" O LEU E 422 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1470 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: 3.87 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 3823 1.37 - 1.51: 3947 1.51 - 1.66: 3502 1.66 - 1.80: 76 1.80 - 1.94: 14 Bond restraints: 11362 Sorted by residual: bond pdb=" O3G AGS E 801 " pdb=" PG AGS E 801 " ideal model delta sigma weight residual 1.558 1.504 0.054 2.00e-02 2.50e+03 7.41e+00 bond pdb=" O3G AGS B 801 " pdb=" PG AGS B 801 " ideal model delta sigma weight residual 1.558 1.504 0.054 2.00e-02 2.50e+03 7.19e+00 bond pdb=" O2G AGS E 801 " pdb=" PG AGS E 801 " ideal model delta sigma weight residual 1.557 1.505 0.052 2.00e-02 2.50e+03 6.74e+00 bond pdb=" O2G AGS B 801 " pdb=" PG AGS B 801 " ideal model delta sigma weight residual 1.557 1.505 0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" O3B AGS E 801 " pdb=" PG AGS E 801 " ideal model delta sigma weight residual 1.559 1.605 -0.046 2.00e-02 2.50e+03 5.20e+00 ... (remaining 11357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 14375 1.72 - 3.45: 928 3.45 - 5.17: 151 5.17 - 6.89: 36 6.89 - 8.62: 26 Bond angle restraints: 15516 Sorted by residual: angle pdb=" N PRO E 455 " pdb=" CA PRO E 455 " pdb=" CB PRO E 455 " ideal model delta sigma weight residual 103.00 110.62 -7.62 1.10e+00 8.26e-01 4.79e+01 angle pdb=" N PRO B 455 " pdb=" CA PRO B 455 " pdb=" CB PRO B 455 " ideal model delta sigma weight residual 103.00 110.58 -7.58 1.10e+00 8.26e-01 4.74e+01 angle pdb=" C TYR E 225 " pdb=" N THR E 226 " pdb=" CA THR E 226 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C TYR B 225 " pdb=" N THR B 226 " pdb=" CA THR B 226 " ideal model delta sigma weight residual 121.54 130.12 -8.58 1.91e+00 2.74e-01 2.02e+01 angle pdb=" N ASN E 185 " pdb=" CA ASN E 185 " pdb=" C ASN E 185 " ideal model delta sigma weight residual 110.42 116.89 -6.47 1.46e+00 4.69e-01 1.96e+01 ... (remaining 15511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.46: 6592 32.46 - 64.92: 184 64.92 - 97.38: 4 97.38 - 129.84: 0 129.84 - 162.30: 2 Dihedral angle restraints: 6782 sinusoidal: 2690 harmonic: 4092 Sorted by residual: dihedral pdb=" CA ARG B 295 " pdb=" C ARG B 295 " pdb=" N SER B 296 " pdb=" CA SER B 296 " ideal model delta harmonic sigma weight residual 180.00 -130.21 -49.79 0 5.00e+00 4.00e-02 9.92e+01 dihedral pdb=" CA ARG E 295 " pdb=" C ARG E 295 " pdb=" N SER E 296 " pdb=" CA SER E 296 " ideal model delta harmonic sigma weight residual -180.00 -130.24 -49.76 0 5.00e+00 4.00e-02 9.90e+01 dihedral pdb=" O1A AGS E 801 " pdb=" O3A AGS E 801 " pdb=" PA AGS E 801 " pdb=" PB AGS E 801 " ideal model delta sinusoidal sigma weight residual -67.73 94.57 -162.30 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 6779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1202 0.047 - 0.094: 402 0.094 - 0.141: 114 0.141 - 0.188: 16 0.188 - 0.235: 4 Chirality restraints: 1738 Sorted by residual: chirality pdb=" CA PRO B 455 " pdb=" N PRO B 455 " pdb=" C PRO B 455 " pdb=" CB PRO B 455 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA PRO E 455 " pdb=" N PRO E 455 " pdb=" C PRO E 455 " pdb=" CB PRO E 455 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PHE B 673 " pdb=" N PHE B 673 " pdb=" C PHE B 673 " pdb=" CB PHE B 673 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.25e-01 ... (remaining 1735 not shown) Planarity restraints: 1980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 451 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.71e+00 pdb=" N PRO E 452 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 452 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 452 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 451 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO B 452 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 452 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 452 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 486 " 0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO E 487 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 487 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 487 " 0.026 5.00e-02 4.00e+02 ... (remaining 1977 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 100 2.63 - 3.20: 10210 3.20 - 3.76: 15367 3.76 - 4.33: 20302 4.33 - 4.90: 35675 Nonbonded interactions: 81654 Sorted by model distance: nonbonded pdb=" O3G AGS B 801 " pdb="MG MG B 802 " model vdw 2.062 2.170 nonbonded pdb=" O3G AGS E 801 " pdb="MG MG E 802 " model vdw 2.063 2.170 nonbonded pdb=" OG SER E 275 " pdb="MG MG E 802 " model vdw 2.069 2.170 nonbonded pdb=" OG SER B 275 " pdb="MG MG B 802 " model vdw 2.070 2.170 nonbonded pdb=" O2B AGS E 801 " pdb="MG MG E 802 " model vdw 2.089 2.170 ... (remaining 81649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'A' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.240 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:17.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 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 : 0.006 0.061 11362 Z= 0.260 Angle : 1.003 8.618 15516 Z= 0.536 Chirality : 0.051 0.235 1738 Planarity : 0.007 0.048 1980 Dihedral : 14.668 162.297 4130 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 2.17 % Allowed : 17.66 % Favored : 80.17 % Rotamer: Outliers : 1.02 % Allowed : 4.32 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.30 (0.18), residues: 1382 helix: -2.03 (0.16), residues: 470 sheet: -1.32 (0.34), residues: 212 loop : -4.10 (0.19), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 297 HIS 0.005 0.001 HIS B 242 PHE 0.017 0.002 PHE E 139 TYR 0.022 0.002 TYR B 685 ARG 0.005 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.16223 ( 496) hydrogen bonds : angle 7.03863 ( 1470) covalent geometry : bond 0.00590 (11362) covalent geometry : angle 1.00268 (15516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 371 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 VAL cc_start: 0.6082 (t) cc_final: 0.5842 (t) REVERT: B 154 VAL cc_start: 0.4398 (OUTLIER) cc_final: 0.4036 (m) REVERT: B 483 PHE cc_start: 0.5060 (m-80) cc_final: 0.4434 (m-80) REVERT: E 154 VAL cc_start: 0.3642 (OUTLIER) cc_final: 0.3332 (m) REVERT: E 354 VAL cc_start: 0.6110 (t) cc_final: 0.5698 (t) outliers start: 12 outliers final: 3 residues processed: 378 average time/residue: 0.9670 time to fit residues: 401.1695 Evaluate side-chains 216 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 211 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 249 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.0570 chunk 81 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 143 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 174 HIS ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN D 21 GLN D 143 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN E 174 HIS E 242 HIS E 334 HIS E 480 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.118924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.096926 restraints weight = 17125.148| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.15 r_work: 0.3207 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 11362 Z= 0.233 Angle : 0.957 12.799 15516 Z= 0.478 Chirality : 0.051 0.229 1738 Planarity : 0.008 0.074 1980 Dihedral : 9.425 161.364 1576 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 4.66 % Allowed : 16.36 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.27 (0.22), residues: 1382 helix: 1.71 (0.22), residues: 480 sheet: -0.89 (0.34), residues: 198 loop : -2.84 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 171 HIS 0.012 0.002 HIS E 484 PHE 0.038 0.003 PHE B 332 TYR 0.018 0.003 TYR E 482 ARG 0.009 0.001 ARG A 160 Details of bonding type rmsd hydrogen bonds : bond 0.04984 ( 496) hydrogen bonds : angle 4.73133 ( 1470) covalent geometry : bond 0.00504 (11362) covalent geometry : angle 0.95692 (15516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6831 (tt0) REVERT: B 190 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: B 389 GLU cc_start: 0.7294 (pt0) cc_final: 0.6542 (pp20) REVERT: B 559 LEU cc_start: 0.7166 (pp) cc_final: 0.6911 (mt) REVERT: D 14 GLU cc_start: 0.7784 (tp30) cc_final: 0.7415 (mm-30) REVERT: E 202 GLU cc_start: 0.8175 (tt0) cc_final: 0.7757 (tm-30) REVERT: E 306 ASP cc_start: 0.7169 (t70) cc_final: 0.6683 (t0) REVERT: E 364 PRO cc_start: 0.6689 (Cg_exo) cc_final: 0.6379 (Cg_endo) REVERT: E 499 GLU cc_start: 0.7158 (pm20) cc_final: 0.6914 (mt-10) REVERT: E 687 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7685 (ttpp) outliers start: 55 outliers final: 16 residues processed: 300 average time/residue: 0.9246 time to fit residues: 308.0041 Evaluate side-chains 232 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 687 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 126 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN B 283 ASN B 327 ASN B 480 GLN D 21 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN E 207 ASN E 283 ASN E 327 ASN E 334 HIS ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 689 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.115337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.093384 restraints weight = 17672.244| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.18 r_work: 0.3157 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11362 Z= 0.199 Angle : 0.824 10.367 15516 Z= 0.404 Chirality : 0.046 0.293 1738 Planarity : 0.007 0.053 1980 Dihedral : 8.717 155.660 1572 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 4.92 % Allowed : 20.93 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.59 (0.23), residues: 1382 helix: 2.38 (0.22), residues: 490 sheet: -0.79 (0.33), residues: 220 loop : -2.55 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 171 HIS 0.044 0.003 HIS B 174 PHE 0.023 0.002 PHE A 107 TYR 0.024 0.002 TYR D 170 ARG 0.009 0.001 ARG E 201 Details of bonding type rmsd hydrogen bonds : bond 0.05663 ( 496) hydrogen bonds : angle 4.54753 ( 1470) covalent geometry : bond 0.00444 (11362) covalent geometry : angle 0.82358 (15516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 277 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6027 (tpp) cc_final: 0.4452 (mmt) REVERT: A 14 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: B 137 GLU cc_start: 0.7316 (pm20) cc_final: 0.6719 (pm20) REVERT: B 190 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: B 302 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8252 (t) REVERT: B 485 LEU cc_start: 0.8321 (tt) cc_final: 0.8047 (tp) REVERT: B 630 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8196 (p) REVERT: B 644 ASN cc_start: 0.7059 (t0) cc_final: 0.6780 (p0) REVERT: D 1 MET cc_start: 0.5609 (tpp) cc_final: 0.4893 (mmp) REVERT: D 21 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7533 (mt0) REVERT: D 26 HIS cc_start: 0.8691 (m-70) cc_final: 0.8446 (m90) REVERT: D 362 ILE cc_start: 0.8463 (mt) cc_final: 0.8240 (tt) REVERT: E 151 GLN cc_start: 0.7930 (tt0) cc_final: 0.7474 (tt0) REVERT: E 200 LEU cc_start: 0.8275 (tp) cc_final: 0.8053 (tp) REVERT: E 202 GLU cc_start: 0.8458 (tt0) cc_final: 0.7866 (tm-30) REVERT: E 251 GLU cc_start: 0.8539 (tt0) cc_final: 0.7923 (pt0) REVERT: E 300 VAL cc_start: 0.8282 (t) cc_final: 0.7889 (p) REVERT: E 312 PHE cc_start: 0.8090 (m-80) cc_final: 0.7797 (m-80) REVERT: E 364 PRO cc_start: 0.7364 (Cg_exo) cc_final: 0.7146 (Cg_endo) REVERT: E 449 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8553 (p) REVERT: E 500 TRP cc_start: 0.8990 (m-90) cc_final: 0.8672 (m-90) outliers start: 58 outliers final: 22 residues processed: 319 average time/residue: 1.0642 time to fit residues: 377.3538 Evaluate side-chains 253 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 639 SER Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 513 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 86 optimal weight: 0.0570 chunk 72 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 124 optimal weight: 0.1980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS B 222 GLN B 689 ASN D 21 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 HIS ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.115846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.094212 restraints weight = 17466.615| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.17 r_work: 0.3169 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.7414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11362 Z= 0.138 Angle : 0.738 9.415 15516 Z= 0.358 Chirality : 0.043 0.200 1738 Planarity : 0.006 0.053 1980 Dihedral : 8.648 154.309 1570 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 4.75 % Allowed : 25.08 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.06 (0.23), residues: 1382 helix: 2.88 (0.22), residues: 480 sheet: -0.49 (0.35), residues: 220 loop : -2.20 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 168 HIS 0.006 0.001 HIS E 174 PHE 0.016 0.002 PHE B 312 TYR 0.013 0.002 TYR B 626 ARG 0.008 0.001 ARG E 201 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 496) hydrogen bonds : angle 4.17415 ( 1470) covalent geometry : bond 0.00310 (11362) covalent geometry : angle 0.73751 (15516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 232 time to evaluate : 1.311 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6041 (tpp) cc_final: 0.4992 (mmt) REVERT: A 349 LEU cc_start: 0.8804 (tt) cc_final: 0.8542 (tm) REVERT: B 151 GLN cc_start: 0.8244 (tt0) cc_final: 0.7831 (tt0) REVERT: B 174 HIS cc_start: 0.7947 (t-90) cc_final: 0.7689 (t-90) REVERT: B 190 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: B 251 GLU cc_start: 0.8513 (tt0) cc_final: 0.7910 (pt0) REVERT: B 302 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8198 (t) REVERT: B 485 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8029 (tp) REVERT: B 629 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8700 (tp) REVERT: B 630 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8326 (p) REVERT: B 644 ASN cc_start: 0.7050 (t0) cc_final: 0.6669 (p0) REVERT: D 5 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8623 (pt) REVERT: D 26 HIS cc_start: 0.8678 (m-70) cc_final: 0.8468 (m90) REVERT: D 349 LEU cc_start: 0.8908 (tp) cc_final: 0.8692 (tt) REVERT: E 251 GLU cc_start: 0.8588 (tt0) cc_final: 0.7971 (pt0) REVERT: E 611 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8618 (mm) REVERT: E 629 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8690 (tp) outliers start: 56 outliers final: 21 residues processed: 274 average time/residue: 1.0344 time to fit residues: 312.1401 Evaluate side-chains 245 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 150 HIS Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 684 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 388 GLN B 533 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN E 171 HIS ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 HIS E 454 GLN E 533 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.111055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.089198 restraints weight = 17575.053| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.08 r_work: 0.3076 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.9575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11362 Z= 0.229 Angle : 0.808 9.594 15516 Z= 0.401 Chirality : 0.047 0.187 1738 Planarity : 0.007 0.049 1980 Dihedral : 8.605 149.017 1568 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 5.51 % Allowed : 26.02 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.38 (0.23), residues: 1382 helix: 2.22 (0.22), residues: 492 sheet: -0.78 (0.31), residues: 246 loop : -2.12 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 500 HIS 0.012 0.002 HIS E 334 PHE 0.025 0.002 PHE D 107 TYR 0.016 0.002 TYR B 382 ARG 0.010 0.001 ARG E 201 Details of bonding type rmsd hydrogen bonds : bond 0.06207 ( 496) hydrogen bonds : angle 4.40076 ( 1470) covalent geometry : bond 0.00552 (11362) covalent geometry : angle 0.80844 (15516) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 266 time to evaluate : 1.270 Fit side-chains REVERT: A 23 TYR cc_start: 0.8717 (m-80) cc_final: 0.8355 (m-80) REVERT: A 349 LEU cc_start: 0.9192 (tt) cc_final: 0.8923 (tm) REVERT: B 151 GLN cc_start: 0.8339 (tt0) cc_final: 0.7737 (tt0) REVERT: B 200 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8636 (tp) REVERT: B 202 GLU cc_start: 0.8682 (tt0) cc_final: 0.8365 (tp30) REVERT: B 205 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8638 (ttp80) REVERT: B 251 GLU cc_start: 0.8553 (tt0) cc_final: 0.7963 (tm-30) REVERT: B 384 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7569 (ttp-110) REVERT: B 407 ASP cc_start: 0.8908 (t0) cc_final: 0.8700 (m-30) REVERT: B 485 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8726 (tp) REVERT: B 560 ARG cc_start: 0.7669 (tmm-80) cc_final: 0.7405 (ttp80) REVERT: B 623 SER cc_start: 0.9077 (t) cc_final: 0.8669 (p) REVERT: B 644 ASN cc_start: 0.7803 (t0) cc_final: 0.6897 (p0) REVERT: D 1 MET cc_start: 0.6255 (tpp) cc_final: 0.5909 (OUTLIER) REVERT: D 23 TYR cc_start: 0.8715 (m-80) cc_final: 0.8504 (m-80) REVERT: D 129 LYS cc_start: 0.8548 (tttt) cc_final: 0.8285 (ttpp) REVERT: D 349 LEU cc_start: 0.9305 (tp) cc_final: 0.9072 (tm) REVERT: E 132 SER cc_start: 0.7667 (OUTLIER) cc_final: 0.7363 (p) REVERT: E 202 GLU cc_start: 0.8722 (tt0) cc_final: 0.8496 (tp30) REVERT: E 251 GLU cc_start: 0.8533 (tt0) cc_final: 0.8001 (pt0) REVERT: E 320 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6992 (pt) REVERT: E 321 THR cc_start: 0.8857 (m) cc_final: 0.8516 (p) REVERT: E 351 MET cc_start: 0.8202 (mtt) cc_final: 0.7970 (mtt) REVERT: E 407 ASP cc_start: 0.8868 (t0) cc_final: 0.8616 (m-30) REVERT: E 623 SER cc_start: 0.9078 (t) cc_final: 0.8729 (p) REVERT: E 644 ASN cc_start: 0.7480 (m110) cc_final: 0.7023 (m-40) outliers start: 65 outliers final: 20 residues processed: 315 average time/residue: 1.0219 time to fit residues: 352.2359 Evaluate side-chains 222 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 150 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 639 SER Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 450 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 45 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 128 optimal weight: 0.1980 chunk 102 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 61 optimal weight: 0.0170 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 ASN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 HIS ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 480 GLN ** E 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.114491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.092222 restraints weight = 17537.510| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.14 r_work: 0.3133 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.9855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11362 Z= 0.132 Angle : 0.735 9.623 15516 Z= 0.355 Chirality : 0.043 0.147 1738 Planarity : 0.006 0.072 1980 Dihedral : 8.324 146.732 1568 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.66 % Allowed : 30.08 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.12 (0.24), residues: 1382 helix: 2.83 (0.23), residues: 480 sheet: -0.72 (0.32), residues: 250 loop : -1.82 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 400 HIS 0.005 0.001 HIS E 334 PHE 0.027 0.002 PHE B 312 TYR 0.014 0.002 TYR B 225 ARG 0.009 0.001 ARG E 560 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 496) hydrogen bonds : angle 3.99763 ( 1470) covalent geometry : bond 0.00294 (11362) covalent geometry : angle 0.73482 (15516) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 210 time to evaluate : 1.352 Fit side-chains REVERT: A 23 TYR cc_start: 0.8640 (m-80) cc_final: 0.8280 (m-80) REVERT: A 139 GLU cc_start: 0.8797 (tt0) cc_final: 0.8596 (tt0) REVERT: A 349 LEU cc_start: 0.9208 (tt) cc_final: 0.8984 (tm) REVERT: B 131 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7155 (pp) REVERT: B 151 GLN cc_start: 0.8309 (tt0) cc_final: 0.7973 (tt0) REVERT: B 200 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8636 (tp) REVERT: B 202 GLU cc_start: 0.8716 (tt0) cc_final: 0.8452 (tp30) REVERT: B 251 GLU cc_start: 0.8507 (tt0) cc_final: 0.8058 (pt0) REVERT: B 422 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8329 (mp) REVERT: B 485 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8616 (tp) REVERT: B 560 ARG cc_start: 0.7681 (tmm-80) cc_final: 0.7437 (ttp80) REVERT: B 623 SER cc_start: 0.9063 (t) cc_final: 0.8620 (p) REVERT: B 644 ASN cc_start: 0.7728 (t0) cc_final: 0.6858 (p0) REVERT: D 129 LYS cc_start: 0.8555 (tttt) cc_final: 0.8310 (ttpp) REVERT: D 349 LEU cc_start: 0.9273 (tp) cc_final: 0.9053 (tm) REVERT: E 131 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7489 (pp) REVERT: E 202 GLU cc_start: 0.8857 (tt0) cc_final: 0.8585 (tp30) REVERT: E 251 GLU cc_start: 0.8527 (tt0) cc_final: 0.8022 (pt0) REVERT: E 321 THR cc_start: 0.8770 (m) cc_final: 0.8510 (p) REVERT: E 351 MET cc_start: 0.8047 (mtt) cc_final: 0.7827 (mtt) REVERT: E 407 ASP cc_start: 0.8862 (t0) cc_final: 0.8652 (m-30) REVERT: E 450 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7873 (mmt) REVERT: E 532 HIS cc_start: 0.8421 (t-90) cc_final: 0.8089 (t-90) REVERT: E 543 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8263 (tp) REVERT: E 556 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8863 (mmmm) REVERT: E 623 SER cc_start: 0.9051 (t) cc_final: 0.8654 (p) outliers start: 55 outliers final: 18 residues processed: 247 average time/residue: 1.0148 time to fit residues: 274.5453 Evaluate side-chains 215 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 150 HIS Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 450 MET Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 684 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 GLN B 689 ASN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 HIS E 480 GLN ** E 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.110388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.088283 restraints weight = 17688.832| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.11 r_work: 0.3067 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 1.0364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11362 Z= 0.185 Angle : 0.748 9.584 15516 Z= 0.366 Chirality : 0.044 0.130 1738 Planarity : 0.006 0.071 1980 Dihedral : 8.254 144.787 1568 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.07 % Allowed : 30.85 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.12 (0.23), residues: 1382 helix: 2.73 (0.23), residues: 480 sheet: -0.37 (0.35), residues: 208 loop : -1.82 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 169 HIS 0.007 0.001 HIS B 532 PHE 0.030 0.002 PHE B 312 TYR 0.023 0.002 TYR E 382 ARG 0.010 0.001 ARG E 237 Details of bonding type rmsd hydrogen bonds : bond 0.05354 ( 496) hydrogen bonds : angle 4.06207 ( 1470) covalent geometry : bond 0.00441 (11362) covalent geometry : angle 0.74848 (15516) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 1.493 Fit side-chains REVERT: A 23 TYR cc_start: 0.8754 (m-80) cc_final: 0.8372 (m-80) REVERT: A 349 LEU cc_start: 0.9265 (tt) cc_final: 0.9038 (tm) REVERT: B 131 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7302 (pp) REVERT: B 151 GLN cc_start: 0.8313 (tt0) cc_final: 0.7960 (tt0) REVERT: B 200 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8708 (tp) REVERT: B 251 GLU cc_start: 0.8511 (tt0) cc_final: 0.8051 (pt0) REVERT: B 485 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8746 (mt) REVERT: B 557 GLU cc_start: 0.7328 (pp20) cc_final: 0.6900 (pp20) REVERT: B 560 ARG cc_start: 0.7894 (tmm-80) cc_final: 0.7453 (ttp80) REVERT: B 623 SER cc_start: 0.9092 (t) cc_final: 0.8864 (t) REVERT: B 644 ASN cc_start: 0.8018 (t0) cc_final: 0.7202 (p0) REVERT: D 23 TYR cc_start: 0.8686 (m-80) cc_final: 0.8149 (m-80) REVERT: D 139 GLU cc_start: 0.8798 (tt0) cc_final: 0.8588 (tp30) REVERT: D 349 LEU cc_start: 0.9369 (tp) cc_final: 0.9152 (tm) REVERT: E 131 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7432 (pp) REVERT: E 251 GLU cc_start: 0.8507 (tt0) cc_final: 0.8027 (pt0) REVERT: E 321 THR cc_start: 0.8842 (m) cc_final: 0.8520 (p) REVERT: E 532 HIS cc_start: 0.8458 (t-90) cc_final: 0.8090 (t-90) REVERT: E 543 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8387 (tp) REVERT: E 556 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8930 (mmmm) REVERT: E 557 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6896 (pp20) REVERT: E 623 SER cc_start: 0.9083 (t) cc_final: 0.8830 (t) REVERT: E 630 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8520 (p) REVERT: E 644 ASN cc_start: 0.7527 (m110) cc_final: 0.7023 (m-40) outliers start: 48 outliers final: 21 residues processed: 229 average time/residue: 1.0827 time to fit residues: 270.7545 Evaluate side-chains 219 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 557 GLU Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain E residue 684 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 110 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 ASN D 3 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 HIS E 480 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.105916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.083949 restraints weight = 17771.372| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.10 r_work: 0.2989 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 1.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 11362 Z= 0.274 Angle : 0.822 10.121 15516 Z= 0.403 Chirality : 0.048 0.150 1738 Planarity : 0.007 0.070 1980 Dihedral : 8.603 145.863 1568 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 4.83 % Allowed : 30.42 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.25 (0.23), residues: 1382 helix: 2.23 (0.22), residues: 492 sheet: -0.33 (0.36), residues: 206 loop : -2.06 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 400 HIS 0.007 0.001 HIS B 334 PHE 0.032 0.002 PHE B 312 TYR 0.026 0.003 TYR E 382 ARG 0.009 0.001 ARG E 201 Details of bonding type rmsd hydrogen bonds : bond 0.06683 ( 496) hydrogen bonds : angle 4.35742 ( 1470) covalent geometry : bond 0.00669 (11362) covalent geometry : angle 0.82218 (15516) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 198 time to evaluate : 1.198 Fit side-chains REVERT: A 351 ASP cc_start: 0.8391 (t0) cc_final: 0.8060 (t0) REVERT: B 131 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7468 (pp) REVERT: B 151 GLN cc_start: 0.8298 (tt0) cc_final: 0.7875 (tt0) REVERT: B 174 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.7603 (t-170) REVERT: B 185 ASN cc_start: 0.8565 (p0) cc_final: 0.8280 (p0) REVERT: B 200 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8834 (tp) REVERT: B 251 GLU cc_start: 0.8524 (tt0) cc_final: 0.7979 (tm-30) REVERT: B 351 MET cc_start: 0.8632 (mtm) cc_final: 0.8352 (mtt) REVERT: B 438 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8552 (tm-30) REVERT: B 446 ILE cc_start: 0.8964 (mt) cc_final: 0.8689 (mm) REVERT: B 485 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8826 (mt) REVERT: B 557 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7309 (pp20) REVERT: B 560 ARG cc_start: 0.7987 (tmm-80) cc_final: 0.7563 (ttp80) REVERT: B 623 SER cc_start: 0.9168 (t) cc_final: 0.8928 (t) REVERT: B 644 ASN cc_start: 0.8177 (t0) cc_final: 0.7356 (p0) REVERT: E 131 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7573 (pp) REVERT: E 174 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7820 (t-90) REVERT: E 206 LEU cc_start: 0.8997 (mt) cc_final: 0.8796 (mp) REVERT: E 251 GLU cc_start: 0.8512 (tt0) cc_final: 0.7890 (tm-30) REVERT: E 309 GLN cc_start: 0.8716 (tt0) cc_final: 0.8297 (mt0) REVERT: E 321 THR cc_start: 0.8903 (m) cc_final: 0.8587 (p) REVERT: E 446 ILE cc_start: 0.8887 (mt) cc_final: 0.8614 (mm) REVERT: E 556 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8870 (mmmm) REVERT: E 557 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7239 (pp20) REVERT: E 623 SER cc_start: 0.9158 (t) cc_final: 0.8935 (t) REVERT: E 630 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8583 (p) REVERT: E 644 ASN cc_start: 0.7647 (m110) cc_final: 0.7174 (m-40) outliers start: 57 outliers final: 30 residues processed: 235 average time/residue: 1.0434 time to fit residues: 268.3045 Evaluate side-chains 218 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 174 HIS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 396 ASN Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 557 GLU Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain E residue 684 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 75 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 0.0770 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS B 111 HIS B 122 GLN ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 ASN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 HIS E 480 GLN ** E 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.110898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.088781 restraints weight = 17452.992| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.11 r_work: 0.3073 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 1.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11362 Z= 0.134 Angle : 0.741 11.397 15516 Z= 0.356 Chirality : 0.043 0.147 1738 Planarity : 0.006 0.063 1980 Dihedral : 8.276 143.060 1568 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.47 % Allowed : 32.29 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.11 (0.23), residues: 1382 helix: 2.73 (0.23), residues: 480 sheet: -0.33 (0.36), residues: 204 loop : -1.85 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 168 HIS 0.005 0.001 HIS E 334 PHE 0.028 0.001 PHE B 312 TYR 0.017 0.002 TYR E 423 ARG 0.008 0.001 ARG E 384 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 496) hydrogen bonds : angle 4.05743 ( 1470) covalent geometry : bond 0.00307 (11362) covalent geometry : angle 0.74139 (15516) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 1.386 Fit side-chains REVERT: A 362 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8952 (pt) REVERT: B 131 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7161 (pp) REVERT: B 151 GLN cc_start: 0.8269 (tt0) cc_final: 0.7975 (tt0) REVERT: B 251 GLU cc_start: 0.8498 (tt0) cc_final: 0.7917 (tm-30) REVERT: B 351 MET cc_start: 0.8514 (mtm) cc_final: 0.8203 (mtt) REVERT: B 446 ILE cc_start: 0.8881 (mt) cc_final: 0.8612 (mm) REVERT: B 556 LYS cc_start: 0.9204 (mtpp) cc_final: 0.8902 (mmmm) REVERT: B 557 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7383 (pp20) REVERT: B 560 ARG cc_start: 0.7919 (tmm-80) cc_final: 0.7656 (ttp80) REVERT: B 623 SER cc_start: 0.9056 (t) cc_final: 0.8682 (t) REVERT: B 626 TYR cc_start: 0.7856 (m-80) cc_final: 0.7522 (m-80) REVERT: B 644 ASN cc_start: 0.8234 (t0) cc_final: 0.7418 (p0) REVERT: D 352 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8365 (mt-10) REVERT: D 362 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8953 (pt) REVERT: E 131 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7466 (pp) REVERT: E 174 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7697 (t-90) REVERT: E 251 GLU cc_start: 0.8502 (tt0) cc_final: 0.7811 (tm-30) REVERT: E 321 THR cc_start: 0.8818 (m) cc_final: 0.8565 (p) REVERT: E 401 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8563 (pp) REVERT: E 446 ILE cc_start: 0.8778 (mt) cc_final: 0.8474 (mm) REVERT: E 556 LYS cc_start: 0.9195 (mmmm) cc_final: 0.8827 (mmmm) REVERT: E 557 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7208 (pp20) REVERT: E 623 SER cc_start: 0.9062 (t) cc_final: 0.8825 (t) REVERT: E 626 TYR cc_start: 0.7804 (m-80) cc_final: 0.7437 (m-80) REVERT: E 644 ASN cc_start: 0.7603 (m110) cc_final: 0.7126 (m-40) outliers start: 41 outliers final: 20 residues processed: 215 average time/residue: 1.4724 time to fit residues: 343.5681 Evaluate side-chains 210 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 174 HIS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 396 ASN Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 557 GLU Chi-restraints excluded: chain E residue 684 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 7 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 68 optimal weight: 0.0040 chunk 47 optimal weight: 1.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 HIS E 480 GLN ** E 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.111230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.089036 restraints weight = 17446.882| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.11 r_work: 0.3079 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 1.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11362 Z= 0.139 Angle : 0.746 12.134 15516 Z= 0.353 Chirality : 0.043 0.159 1738 Planarity : 0.006 0.062 1980 Dihedral : 8.169 141.952 1568 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.22 % Allowed : 32.46 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.24 (0.23), residues: 1382 helix: 2.87 (0.23), residues: 480 sheet: -0.26 (0.36), residues: 204 loop : -1.79 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 168 HIS 0.005 0.001 HIS E 171 PHE 0.028 0.001 PHE B 312 TYR 0.023 0.002 TYR E 145 ARG 0.009 0.001 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 496) hydrogen bonds : angle 3.98379 ( 1470) covalent geometry : bond 0.00323 (11362) covalent geometry : angle 0.74609 (15516) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 2.198 Fit side-chains REVERT: A 141 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.7941 (tmm-80) REVERT: A 362 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8944 (pt) REVERT: B 131 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7093 (pp) REVERT: B 151 GLN cc_start: 0.8205 (tt0) cc_final: 0.7859 (tt0) REVERT: B 174 HIS cc_start: 0.8085 (OUTLIER) cc_final: 0.7472 (t-90) REVERT: B 187 THR cc_start: 0.7468 (m) cc_final: 0.7132 (m) REVERT: B 251 GLU cc_start: 0.8517 (tt0) cc_final: 0.7906 (tm-30) REVERT: B 351 MET cc_start: 0.8386 (mtm) cc_final: 0.8085 (mtt) REVERT: B 446 ILE cc_start: 0.8865 (mt) cc_final: 0.8613 (mm) REVERT: B 556 LYS cc_start: 0.9205 (mtpp) cc_final: 0.8901 (mmmm) REVERT: B 557 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7535 (pp20) REVERT: B 560 ARG cc_start: 0.7987 (tmm-80) cc_final: 0.7736 (ttp80) REVERT: B 623 SER cc_start: 0.9029 (t) cc_final: 0.8783 (t) REVERT: B 626 TYR cc_start: 0.7858 (m-80) cc_final: 0.7321 (m-80) REVERT: B 644 ASN cc_start: 0.8226 (t0) cc_final: 0.7421 (p0) REVERT: D 352 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8413 (mt-10) REVERT: D 362 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8968 (pt) REVERT: E 131 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7307 (OUTLIER) REVERT: E 174 HIS cc_start: 0.8024 (OUTLIER) cc_final: 0.7684 (t-90) REVERT: E 201 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8254 (mtp85) REVERT: E 251 GLU cc_start: 0.8482 (tt0) cc_final: 0.7814 (tm-30) REVERT: E 309 GLN cc_start: 0.8569 (tt0) cc_final: 0.8277 (mt0) REVERT: E 321 THR cc_start: 0.8799 (m) cc_final: 0.8534 (p) REVERT: E 401 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8562 (pp) REVERT: E 446 ILE cc_start: 0.8791 (mt) cc_final: 0.8487 (mm) REVERT: E 556 LYS cc_start: 0.9138 (mmmm) cc_final: 0.8789 (mmmm) REVERT: E 557 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7299 (pp20) REVERT: E 623 SER cc_start: 0.9043 (t) cc_final: 0.8720 (t) REVERT: E 644 ASN cc_start: 0.7655 (m110) cc_final: 0.7183 (m-40) outliers start: 38 outliers final: 19 residues processed: 211 average time/residue: 1.5836 time to fit residues: 363.7556 Evaluate side-chains 202 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 174 HIS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 480 GLN Chi-restraints excluded: chain E residue 557 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 75 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.110826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.088752 restraints weight = 17420.244| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.10 r_work: 0.3078 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 1.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 11362 Z= 0.191 Angle : 0.984 59.200 15516 Z= 0.528 Chirality : 0.048 0.863 1738 Planarity : 0.006 0.062 1980 Dihedral : 8.167 141.955 1568 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.63 % Allowed : 32.63 % Favored : 64.75 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.23 (0.23), residues: 1382 helix: 2.84 (0.23), residues: 480 sheet: -0.26 (0.36), residues: 204 loop : -1.78 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 168 HIS 0.004 0.001 HIS B 532 PHE 0.026 0.001 PHE B 312 TYR 0.017 0.002 TYR E 382 ARG 0.007 0.001 ARG E 201 Details of bonding type rmsd hydrogen bonds : bond 0.04579 ( 496) hydrogen bonds : angle 3.98432 ( 1470) covalent geometry : bond 0.00415 (11362) covalent geometry : angle 0.98389 (15516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8333.28 seconds wall clock time: 152 minutes 19.67 seconds (9139.67 seconds total)